Package 'idr2d'

Title: Irreproducible Discovery Rate for Genomic Interactions Data
Description: A tool to measure reproducibility between genomic experiments that produce two-dimensional peaks (interactions between peaks), such as ChIA-PET, HiChIP, and HiC. idr2d is an extension of the original idr package, which is intended for (one-dimensional) ChIP-seq peaks.
Authors: Konstantin Krismer [aut, cre, cph] , David Gifford [ths, cph]
Maintainer: Konstantin Krismer <[email protected]>
License: MIT + file LICENSE
Version: 1.21.0
Built: 2024-10-31 06:08:47 UTC
Source: https://github.com/bioc/idr2d

Help Index

Distance between Midpoints of two Peaks

Description

Calculates the distance in nucleotides between the midpoints of two peaks.

Note: peaks must be on the same chromosome; start coordinate is always less than end coordinate

Usage

calculate_midpoint_distance1d(peak1_start, peak1_end, peak2_start, peak2_end)

Arguments

peak1_start

integer vector; genomic start coordinate(s) of peak in replicate 1
peak1_end

integer vector; genomic end coordinate(s) of peak in replicate 1
peak2_start

integer vector; genomic start coordinate(s) of peak in replicate 2
peak2_end

integer vector; genomic end coordinate(s) of peak in replicate 2

Value

positive integer vector; distances between peak pairs

Examples

# identical, zero distance
calculate_midpoint_distance1d(100, 120,
                          100, 120)

# centered, zero distance
calculate_midpoint_distance1d(100, 120,
                          90, 130)

# off by 10 per anchor
calculate_midpoint_distance1d(100, 120,
                         110, 130)

# vectorized example
calculate_midpoint_distance1d(c(100, 100, 100),
                          c(120, 120, 120),
                          c(100, 90, 110),
                          c(120, 130, 130))

Distance between Anchor Midpoints of two Interactions

Description

Calculates the distance in nucleotides between the anchor midpoints of two interactions, which is the sum of the distance between midpoints of anchor A in interaction 1 and anchor A in interaction 2, and the distance between midpoints of anchor B in interaction 1 and anchor B in interaction 2.

Note: all anchors must be on the same chromosome; start coordinate is always less than end coordinate

Usage

calculate_midpoint_distance2d(
  int1_anchor_a_start,
  int1_anchor_a_end,
  int1_anchor_b_start,
  int1_anchor_b_end,
  int2_anchor_a_start,
  int2_anchor_a_end,
  int2_anchor_b_start,
  int2_anchor_b_end
)

Arguments

int1_anchor_a_start

integer vector; genomic start coordinate(s) of anchor A in replicate 1 interaction
int1_anchor_a_end

integer vector; genomic end coordinate(s) of anchor A in replicate 1 interaction
int1_anchor_b_start

integer vector; genomic start coordinate(s) of anchor B in replicate 1 interaction
int1_anchor_b_end

integer vector; genomic end coordinate(s) of anchor B in replicate 1 interaction
int2_anchor_a_start

integer vector; genomic start coordinate(s) of anchor A in replicate 2 interaction
int2_anchor_a_end

integer vector; genomic end coordinate(s) of anchor A in replicate 2 interaction
int2_anchor_b_start

integer vector; genomic start coordinate(s) of anchor B in replicate 2 interaction
int2_anchor_b_end

integer vector; genomic end coordinate(s) of anchor B in replicate 2 interaction

Value

positive integer vector; distances between interaction pairs

Examples

# identical, zero distance
calculate_midpoint_distance2d(100, 120, 240, 260,
                              100, 120, 240, 260)

# centered, zero distance
calculate_midpoint_distance2d(100, 120, 240, 260,
                              90, 130, 230, 270)

# off by 10 per anchor
calculate_midpoint_distance2d(100, 120, 240, 250,
                              110, 130, 230, 240)

# off by 10 (anchor B only)
calculate_midpoint_distance2d(100, 120, 240, 250,
                              90, 130, 250, 260)

# vectorized example
calculate_midpoint_distance2d(c(100, 100, 100, 100),
                              c(120, 120, 120, 120),
                              c(240, 240, 240, 240),
                              c(260, 260, 250, 250),
                              c(100, 90, 110, 90),
                              c(120, 130, 130, 130),
                              c(240, 230, 230, 250),
                              c(260, 270, 240, 260))

Relative Anchor Overlap of two Peaks

Description

Calculates the overlap between anchor A of interaction 1 and anchor A of interaction 2, as well as anchor B of interaction 1 and anchor B of interaction 2. The overlap (in nucleotides) is then normalized by the length of the anchors.

Usage

calculate_relative_overlap1d(peak1_start, peak1_end, peak2_start, peak2_end)

Arguments

peak1_start

integer vector; genomic start coordinate(s) of peak in replicate 1
peak1_end

integer vector; genomic end coordinate(s) of peak in replicate 1
peak2_start

integer vector; genomic start coordinate(s) of peak in replicate 2
peak2_end

integer vector; genomic end coordinate(s) of peak in replicate 2

Value

numeric vector; relative overlaps between peak pairs

Examples

# 100% overlap
calculate_relative_overlap1d(100, 120,
                         100, 120)

# 50% overlap
calculate_relative_overlap1d(100, 120,
                         100, 110)

# negative overlap
calculate_relative_overlap1d(100, 120,
                         130, 140)

# larger negative overlap
calculate_relative_overlap1d(100, 120,
                         200, 220)

# vectorized example
calculate_relative_overlap1d(c(100, 100, 100, 100),
                         c(120, 120, 120, 120),
                         c(100, 100, 130, 200),
                         c(120, 110, 140, 220))

Relative Anchor Overlap of two Interactions

Description

Calculates the overlap between anchor A of interaction 1 and anchor A of interaction 2, as well as anchor B of interaction 1 and anchor B of interaction 2. The overlap (in nucleotides) is then normalized by the length of the anchors.

Note: anchors A and B of the same interaction have to be on the same chromosome; start coordinate is always less than end coordinate

Usage

calculate_relative_overlap2d(
  int1_anchor_a_start,
  int1_anchor_a_end,
  int1_anchor_b_start,
  int1_anchor_b_end,
  int2_anchor_a_start,
  int2_anchor_a_end,
  int2_anchor_b_start,
  int2_anchor_b_end
)

Arguments

int1_anchor_a_start

integer vector; genomic start coordinate(s) of anchor A in replicate 1 interaction
int1_anchor_a_end

integer vector; genomic end coordinate(s) of anchor A in replicate 1 interaction
int1_anchor_b_start

integer vector; genomic start coordinate(s) of anchor B in replicate 1 interaction
int1_anchor_b_end

integer vector; genomic end coordinate(s) of anchor B in replicate 1 interaction
int2_anchor_a_start

integer vector; genomic start coordinate(s) of anchor A in replicate 2 interaction
int2_anchor_a_end

integer vector; genomic end coordinate(s) of anchor A in replicate 2 interaction
int2_anchor_b_start

integer vector; genomic start coordinate(s) of anchor B in replicate 2 interaction
int2_anchor_b_end

integer vector; genomic end coordinate(s) of anchor B in replicate 2 interaction

Value

numeric vector; relative overlaps between interaction pairs

Examples

# 100% overlap
calculate_relative_overlap2d(100, 120, 240, 260,
                             100, 120, 240, 260)

# 50% overlap
calculate_relative_overlap2d(100, 120, 240, 250,
                             100, 110, 240, 260)

# negative overlap
calculate_relative_overlap2d(100, 120, 240, 250,
                             130, 140, 260, 280)

# larger negative overlap
calculate_relative_overlap2d(100, 120, 240, 250,
                             200, 220, 340, 350)

# vectorized example
calculate_relative_overlap2d(c(100, 100, 100, 100),
                             c(120, 120, 120, 120),
                             c(240, 240, 240, 240),
                             c(260, 250, 250, 250),
                             c(100, 100, 130, 200),
                             c(120, 110, 140, 220),
                             c(240, 240, 260, 340),
                             c(260, 260, 280, 350))

Example Genomic Interaction Data Set

Description

This object contains genomic interactions on chromosomes 1 to 5, which could be the results of Hi-C or ChIA-PET experiments, done in duplicates.

Usage

chiapet

Format

A list with two components, the data frames rep1_df and rep2_df, which have the following seven columns:

column 1: chr_a character; genomic location of anchor A - chromosome (e.g., "chr3")
column 2: start_a integer; genomic location of anchor A - start coordinate
column 3: end_a integer; genomic location of anchor A - end coordinate
column 4: chr_b character; genomic location of anchor B - chromosome (e.g., "chr3")
column 5: start_b integer; genomic location of anchor B - start coordinate
column 6: end_b integer; genomic location of anchor B - end coordinate
column 7: fdr numeric; False Discovery Rate - significance of interaction

Example Genomic Peak Data Set

Description

This object contains genomic peaks from two replicate ChIP-seq experiments.

Usage

chipseq

Format

A list with two components, the data frames rep1_df and rep2_df, which have the following four columns:

column 1: chr character; genomic location of peak - chromosome (e.g., "chr3")
column 2: start integer; genomic location of peak - start coordinate
column 3: end integer; genomic location of peak - end coordinate
column 4: value numeric; heuristic used to rank the peaks

Identifies Overlapping Anchors

Description

Identifies all overlapping anchor pairs (m:n mapping).

Usage

determine_anchor_overlap(rep1_anchor, rep2_anchor, max_gap = -1L)

Arguments

rep1_anchor

data frame with the following columns:

column 1: chr character; genomic location of anchor in replicate 1 - chromosome (e.g., "chr3")
column 2: start integer; genomic location of anchor in replicate 1 - start coordinate
column 3: end integer; genomic location of anchor in replicate 1 - end coordinate
rep2_anchor

data frame with the following columns:

column 1: chr character; genomic location of anchor in replicate 2 - chromosome (e.g., "chr3")
column 2: start integer; genomic location of anchor in replicate 2 - start coordinate
column 3: end integer; genomic location of anchor in replicate 2 - end coordinate
max_gap

integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)

Value

A data frame containing overlapping anchor pairs with the following columns:

column 1: rep1_idx anchor index in data frame rep1_anchor
column 2: rep2_idx anchor index in data frame rep2_anchor

Examples

rep1_df <- idr2d:::chiapet$rep1_df
rep2_df <- idr2d:::chiapet$rep2_df

rep1_anchor_a <- data.frame(chr = rep1_df[, 1],
                            start = rep1_df[, 2],
                            end = rep1_df[, 3])
rep2_anchor_a <- data.frame(chr = rep2_df[, 1],
                            start = rep2_df[, 2],
                            end = rep2_df[, 3])

anchor_a_overlap <- determine_anchor_overlap(rep1_anchor_a, rep2_anchor_a)

Create Hi-C contact map

Description

Creates Hi-C contact maps to visualize the results of estimate_idr2d_hic.

Usage

draw_hic_contact_map(
  df,
  idr_cutoff = NULL,
  chromosome = NULL,
  start_coordinate = NULL,
  end_coordinate = NULL,
  title = NULL,
  values_normalized = FALSE,
  log_values = TRUE
)

Arguments

df

output of estimate_idr2d_hic, a data frame with the following columns:

column 1: interaction character; genomic location of interaction block (e.g., "chr1:204940000-204940000")
column 2: value numeric; p-value, FDR, or heuristic used to rank the interactions
column 3: "rep_value" numeric; value of corresponding replicate interaction
column 4: "rank" integer; rank of the interaction, established by value column, ascending order
column 5: "rep_rank" integer; rank of corresponding replicate interaction
column 6: "idr" integer; IDR of the block and the corresponding block in the other replicate
idr_cutoff

numeric; only show blocks with IDR < idr_cutoff, shows all blocks by default
chromosome

character; chromsome name or list of chromosome names to be analyzed, e.g., UCSC chromosome 1, "chr1", defaults to all chromosomes (chromosome = NULL)
start_coordinate

integer; only show contact map window between "start_coordinate" and "end_coordinate", by default shows entire chromosome
end_coordinate

integer; only show contact map window between "start_coordinate" and "end_coordinate", by default shows entire chromosome
title

character; plot title
values_normalized

logical; are read counts in value column raw or normalized? Defaults to FALSE
log_values

logical; log-transform value column? Defaults to TRUE

Value

ggplot2 object; Hi-C contact map

Examples

idr_results_df <- estimate_idr2d_hic(idr2d:::hic$rep1_df,
                                     idr2d:::hic$rep2_df)
draw_hic_contact_map(idr_results_df, idr_cutoff = 0.05, chromosome = "chr1")

Create histogram of IDR values

Description

Creates diagnostic plots to visualize the results of estimate_idr.

Usage

draw_idr_distribution_histogram(
  df,
  remove_na = TRUE,
  xlab = "IDR",
  ylab = "density",
  title = "IDR value distribution"
)

Arguments

df

part of output of estimate_idr, a data frame with at least the following named columns:

idr IDR of the peak and the corresponding peak in the other replicate.
remove_na

logical; should NA values be removed?
xlab

character; x axis label
ylab

character; y axis label
title

character; plot title

Value

ggplot2 object; IDR distribution histogram

Examples

idr_results <- estimate_idr1d(idr2d:::chipseq$rep1_df,
                              idr2d:::chipseq$rep2_df,
                              value_transformation = "log")
draw_idr_distribution_histogram(idr_results$rep1_df)

Create scatterplot of IDR values

Description

Creates diagnostic plots to visualize the results of estimate_idr.

Usage

draw_rank_idr_scatterplot(
  df,
  remove_na = TRUE,
  xlab = "rank in replicate 1",
  ylab = "rank in replicate 2",
  log_idr = FALSE,
  title = "rank - IDR dependence",
  color_gradient = c("rainbow", "default"),
  alpha = 1,
  max_points_shown = 2500
)

Arguments

df

part of output of estimate_idr, a data frame with at least the following named columns:

rank integer; rank of the peak, established by value column, ascending order
rep_rank integer; rank of corresponding replicate peak.
idr IDR of the peak and the corresponding peak in the other replicate.
remove_na

logical; should NA values be removed?
xlab

character; x axis label
ylab

character; y axis label
log_idr

logical; use logarithmized IDRs for colors to better distinguish highly significant IDRs
title

character; plot title
color_gradient

character; either "rainbow" or "default"
alpha

numeric; transparency of dots, from 0.0 - 1.0, where 1.0 is completely opaque; default is 1.0
max_points_shown

integer; default is 2500

Value

ggplot2 object; IDR rank scatterplot

Examples

idr_results <- estimate_idr1d(idr2d:::chipseq$rep1_df,
                              idr2d:::chipseq$rep2_df,
                              value_transformation = "log")
draw_rank_idr_scatterplot(idr_results$rep1_df)

Create scatterplot of IDR values

Description

Creates diagnostic plots to visualize the results of estimate_idr.

Usage

draw_value_idr_scatterplot(
  df,
  remove_na = TRUE,
  remove_outliers = TRUE,
  xlab = "transformed value in replicate 1",
  ylab = "transformed value in replicate 2",
  log_axes = FALSE,
  log_idr = FALSE,
  title = "value - IDR dependence",
  color_gradient = c("rainbow", "default"),
  alpha = 1,
  max_points_shown = 2500
)

Arguments

df

part of output of estimate_idr, a data frame with at least the following named columns:

value numeric; p-value, FDR, or heuristic used to rank the peaks
rep_value numeric; value of corresponding replicate peak
idr IDR of the peak and the corresponding peak in the other replicate.
remove_na

logical; should NA values be removed?
remove_outliers

logical; removes extreme data points
xlab

character; x axis label
ylab

character; y axis label
log_axes

logical; show logarithmized values from replicate 1 and 2 (default value is FALSE)
log_idr

logical; use logarithmized IDRs for colors to better distinguish highly significant IDRs (default value is FALSE)
title

character; plot title
color_gradient

character; either "rainbow" or "default"
alpha

numeric; transparency of dots, from 0.0 - 1.0, where 1.0 is completely opaque; default is 1.0
max_points_shown

integer; default is 2500

Value

ggplot2 object; IDR value scatterplot

Examples

idr_results <- estimate_idr1d(idr2d:::chipseq$rep1_df,
                              idr2d:::chipseq$rep2_df,
                              value_transformation = "log")
draw_value_idr_scatterplot(idr_results$rep1_df)

Finds One-to-One Correspondence between Peaks or interactions from Replicate 1 and 2

Description

This method establishes a bijective assignment between observations (genomic peaks in case of ChIP-seq, genomic interactions in case of ChIA-PET, HiChIP, and Hi-C) from replicate 1 and 2. An observation in replicate 1 is assigned to an observation in replicate 2 if and only if (1) the observation loci in both replicates overlap (or the gap between them is less than or equal to max_gap), and (2) there is no other observation in replicate 2 that overlaps with the observation in replicate 1 and has a lower ambiguity resolution value.

Usage

establish_bijection(
  rep1_df,
  rep2_df,
  analysis_type = c("IDR1D", "IDR2D"),
  ambiguity_resolution_method = c("overlap", "midpoint", "value"),
  max_gap = -1L
)

Arguments

rep1_df

data frame of observations (i.e., genomic peaks or genomic interactions) of replicate 1. If analysis_type is IDR1D, the columns of rep1_df are described in establish_bijection1d, otherwise in establish_bijection2d
rep2_df

data frame of observations (i.e., genomic peaks or genomic interactions) of replicate 2. Same columns as rep1_df.
analysis_type

"IDR2D" for genomic interaction data sets, "IDR1D" for genomic peak data sets
ambiguity_resolution_method

defines how ambiguous assignments (when one interaction or peak in replicate 1 overlaps with multiple interactions or peaks in replicate 2 or vice versa) are resolved. For available methods, see establish_overlap1d or establish_overlap2d, respectively.
max_gap

integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)

Value

See establish_bijection1d or establish_bijection2d, respectively.

Examples

rep1_df <- idr2d:::chipseq$rep1_df
rep1_df$value <- preprocess(rep1_df$value, "log")

rep2_df <- idr2d:::chipseq$rep2_df
rep2_df$value <- preprocess(rep2_df$value, "log")

mapping <- establish_bijection(rep1_df, rep2_df, analysis_type = "IDR1D")

Finds One-to-One Correspondence between Peaks from Replicate 1 and 2

Description

This method establishes a bijective assignment between peaks from replicate 1 and 2. A peak in replicate 1 is assigned to a peak in replicate 2 if and only if (1) they overlap (or the gap between the peaks is less than or equal to max_gap), and (2) there is no other peak in replicate 2 that overlaps with the peak in replicate 1 and has a lower ambiguity resolution value.

Usage

establish_bijection1d(
  rep1_df,
  rep2_df,
  ambiguity_resolution_method = c("overlap", "midpoint", "value"),
  max_gap = -1L
)

Arguments

rep1_df

data frame of observations (i.e., genomic peaks) of replicate 1, with at least the following columns (position of columns matter, column names are irrelevant):

column 1: chr character; genomic location of peak - chromosome (e.g., "chr3")
column 2: start integer; genomic location of peak - start coordinate
column 3: end integer; genomic location of peak - end coordinate
column 4: value numeric; p-value, FDR, or heuristic used to rank the interactions
rep2_df

data frame of observations (i.e., genomic peaks) of replicate 2, with the following columns (position of columns matter, column names are irrelevant):

column 1: chr character; genomic location of peak - chromosome (e.g., "chr3")
column 2: start integer; genomic location of peak - start coordinate
column 3: end integer; genomic location of peak - end coordinate
column 4: value numeric; p-value, FDR, or heuristic used to rank the interactions
ambiguity_resolution_method

defines how ambiguous assignments (when one interaction in replicate 1 overlaps with multiple interactions in replicate 2 or vice versa) are resolved. Available methods:

"value" interactions are prioritized by ascending or descending value column (see sorting_direction), e.g., if two interactions in replicate 1 overlap with one interaction in replicate 2, the interaction from replicate 1 is chosen which has a lower (if sorting_direction is "ascending") or higher (if "descending") value
"overlap" the interaction pair is chosen which has the highest relative overlap, i.e., overlap in nucleotides of replicate 1 interaction anchor A and replicate 2 interaction anchor A, plus replicate 1 interaction anchor B and replicate 2 interaction anchor B, normalized by their lengths
"midpoint" the interaction pair is chosen which has the smallest distance between their anchor midpoints, i.e., distance from midpoint of replicate 1 interaction anchor A to midpoint of replicate 2 interaction anchor A, plus distance from midpoint of replicate 1 interaction anchor B to midpoint of replicate 2 interaction anchor B
max_gap

integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)

Value

Data frames rep1_df and rep2_df with the following columns:

column 1: chr character; genomic location of peak - chromosome (e.g., "chr3")
column 2: start integer; genomic location of peak - start coordinate
column 3: end integer; genomic location of peak - end coordinate
column 4: value numeric; p-value, FDR, or heuristic used to rank the peaks
column 5: rep_value numeric; value of corresponding replicate peak. If no corresponding peak was found, rep_value is set to NA.
column 6: rank integer; rank of the peak, established by value column, ascending order
column 7: rep_rank integer; rank of corresponding replicate peak. If no corresponding peak was found, rep_rank is set to NA.
column 8: idx integer; peak index, primary key
column 9: rep_idx integer; specifies the index of the corresponding peak in the other replicate (foreign key). If no corresponding peak was found, rep_idx is set to NA.

Examples

rep1_df <- idr2d:::chipseq$rep1_df
rep1_df$value <- preprocess(rep1_df$value, "log")

rep2_df <- idr2d:::chipseq$rep2_df
rep2_df$value <- preprocess(rep2_df$value, "log")

mapping <- establish_bijection1d(rep1_df, rep2_df)

Finds One-to-One Correspondence between Interactions from Replicate 1 and 2

Description

This method establishes a bijective assignment between interactions from replicate 1 and 2. An interaction in replicate 1 is assigned to an interaction in replicate 2 if and only if (1) both anchors of the interactions overlap (or the gap between anchor A/B in replicate 1 and 2 is less than or equal to max_gap), and (2) there is no other interaction in replicate 2 that overlaps with the interaction in replicate 1 and has a lower ambiguity resolution value.

Usage

establish_bijection2d(
  rep1_df,
  rep2_df,
  ambiguity_resolution_method = c("overlap", "midpoint", "value"),
  max_gap = -1L
)

Arguments

rep1_df

data frame of observations (i.e., genomic interactions) of replicate 1, with at least the following columns (position of columns matter, column names are irrelevant):

column 1: chr_a character; genomic location of anchor A - chromosome (e.g., "chr3")
column 2: start_a integer; genomic location of anchor A - start coordinate
column 3: end_a integer; genomic location of anchor A - end coordinate
column 4: chr_b character; genomic location of anchor B - chromosome (e.g., "chr3")
column 5: start_b integer; genomic location of anchor B - start coordinate
column 6: end_b integer; genomic location of anchor B - end coordinate
column 7: value numeric; p-value, FDR, or heuristic used to rank the interactions
rep2_df

data frame of observations (i.e., genomic interactions) of replicate 2, with the following columns (position of columns matter, column names are irrelevant):

column 1: chr_a character; genomic location of anchor A - chromosome (e.g., "chr3")
column 2: start_a integer; genomic location of anchor A - start coordinate
column 3: end_a integer; genomic location of anchor A - end coordinate
column 4: chr_b character; genomic location of anchor B - chromosome (e.g., "chr3")
column 5: start_b integer; genomic location of anchor B - start coordinate
column 6: end_b integer; genomic location of anchor B - end coordinate
column 7: value numeric; p-value, FDR, or heuristic used to rank the interactions
ambiguity_resolution_method

defines how ambiguous assignments (when one interaction in replicate 1 overlaps with multiple interactions in replicate 2 or vice versa) are resolved. Available methods:

"value" interactions are prioritized by ascending or descending value column (see sorting_direction), e.g., if two interactions in replicate 1 overlap with one interaction in replicate 2, the interaction from replicate 1 is chosen which has a lower (if sorting_direction is "ascending") or higher (if "descending") value
"overlap" the interaction pair is chosen which has the highest relative overlap, i.e., overlap in nucleotides of replicate 1 interaction anchor A and replicate 2 interaction anchor A, plus replicate 1 interaction anchor B and replicate 2 interaction anchor B, normalized by their lengths
"midpoint" the interaction pair is chosen which has the smallest distance between their anchor midpoints, i.e., distance from midpoint of replicate 1 interaction anchor A to midpoint of replicate 2 interaction anchor A, plus distance from midpoint of replicate 1 interaction anchor B to midpoint of replicate 2 interaction anchor B
max_gap

integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)

Value

Data frames rep1_df and rep2_df with the following columns:

column 1: chr_a character; genomic location of anchor A - chromosome (e.g., "chr3")
column 2: start_a integer; genomic location of anchor A - start coordinate
column 3: end_a integer; genomic location of anchor A - end coordinate
column 4: chr_b character; genomic location of anchor B - chromosome (e.g., "chr3")
column 5: start_b integer; genomic location of anchor B - start coordinate
column 6: end_b integer; genomic location of anchor B - end coordinate
column 7: value numeric; p-value, FDR, or heuristic used to rank the interactions
column 8: "rep_value" numeric; value of corresponding replicate interaction. If no corresponding interaction was found, rep_value is set to NA.
column 9: "rank" integer; rank of the interaction, established by value column, ascending order
column 10: "rep_rank" integer; rank of corresponding replicate interaction. If no corresponding interaction was found, rep_rank is set to NA.
column 11: "idx" integer; interaction index, primary key
column 12: "rep_idx" integer; specifies the index of the corresponding interaction in the other replicate (foreign key). If no corresponding interaction was found, rep_idx is set to NA.

Examples

rep1_df <- idr2d:::chiapet$rep1_df
rep1_df$fdr <- preprocess(rep1_df$fdr, "log_additive_inverse")

rep2_df <- idr2d:::chiapet$rep2_df
rep2_df$fdr <- preprocess(rep2_df$fdr, "log_additive_inverse")

mapping <- establish_bijection2d(rep1_df, rep2_df)

Establish m:n Mapping Between Peaks from Replicate 1 and 2

Description

This method returns all overlapping interactions between two replicates. For each pair of overlapping interactions, the ambiguity resolution value (ARV) is calculated, which helps to reduce the m:n mapping to a 1:1 mapping. The semantics of the ARV depend on the specified ambiguity_resolution_method, but in general interaction pairs with lower ARVs have priority over interaction pairs with higher ARVs when the bijective mapping is established.

Usage

establish_overlap1d(
  rep1_df,
  rep2_df,
  ambiguity_resolution_method = c("overlap", "midpoint", "value"),
  max_gap = -1L
)

Arguments

rep1_df

data frame of observations (i.e., genomic peaks) of replicate 1, with at least the following columns (position of columns matter, column names are irrelevant):

column 1: chr character; genomic location of peak - chromosome (e.g., "chr3")
column 2: start integer; genomic location of peak - start coordinate
column 3: end integer; genomic location of peak - end coordinate
column 4: value numeric; p-value, FDR, or heuristic used to rank the interactions
rep2_df

data frame of observations (i.e., genomic peaks) of replicate 2, with the following columns (position of columns matter, column names are irrelevant):

column 1: chr character; genomic location of peak - chromosome (e.g., "chr3")
column 2: start integer; genomic location of peak - start coordinate
column 3: end integer; genomic location of peak - end coordinate
column 4: value numeric; p-value, FDR, or heuristic used to rank the interactions
ambiguity_resolution_method

defines how ambiguous assignments (when one interaction in replicate 1 overlaps with multiple interactions in replicate 2 or vice versa) are resolved. Available methods:

"value" interactions are prioritized by ascending or descending value column (see sorting_direction), e.g., if two interactions in replicate 1 overlap with one interaction in replicate 2, the interaction from replicate 1 is chosen which has a lower (if sorting_direction is "ascending") or higher (if "descending") value
"overlap" the interaction pair is chosen which has the highest relative overlap, i.e., overlap in nucleotides of replicate 1 interaction anchor A and replicate 2 interaction anchor A, plus replicate 1 interaction anchor B and replicate 2 interaction anchor B, normalized by their lengths
"midpoint" the interaction pair is chosen which has the smallest distance between their anchor midpoints, i.e., distance from midpoint of replicate 1 interaction anchor A to midpoint of replicate 2 interaction anchor A, plus distance from midpoint of replicate 1 interaction anchor B to midpoint of replicate 2 interaction anchor B
max_gap

integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)

Value

data frame with the following columns:

column 1: rep1_idx index of interaction in replicate 1 (i.e., row index in rep1_df)
column 2: rep2_idx index of interaction in replicate 2 (i.e., row index in rep2_df)
column 3: arv ambiguity resolution value used turn m:n mapping into 1:1 mapping. Interaction pairs with lower arv are prioritized.

Examples

rep1_df <- idr2d:::chipseq$rep1_df
rep1_df$value <- preprocess(rep1_df$value, "log_additive_inverse")

rep2_df <- idr2d:::chipseq$rep2_df
rep2_df$value <- preprocess(rep2_df$value, "log_additive_inverse")

# shuffle to break preexisting order
rep1_df <- rep1_df[sample.int(nrow(rep1_df)), ]
rep2_df <- rep2_df[sample.int(nrow(rep2_df)), ]

# sort by value column
rep1_df <- dplyr::arrange(rep1_df, value)
rep2_df <- dplyr::arrange(rep2_df, value)

pairs_df <- establish_overlap1d(rep1_df, rep2_df)

Establish m:n mapping between interactions from replicate 1 and 2

Description

This method returns all overlapping interactions between two replicates. For each pair of overlapping interactions, the ambiguity resolution value (ARV) is calculated, which helps to reduce the m:n mapping to a 1:1 mapping. The semantics of the ARV depend on the specified ambiguity_resolution_method, but in general interaction pairs with lower ARVs have priority over interaction pairs with higher ARVs when the bijective mapping is established.

Usage

establish_overlap2d(
  rep1_df,
  rep2_df,
  ambiguity_resolution_method = c("overlap", "midpoint", "value"),
  max_gap = -1L
)

Arguments

rep1_df

data frame of observations (i.e., genomic interactions) of replicate 1, with at least the following columns (position of columns matter, column names are irrelevant):

column 1: chr_a character; genomic location of anchor A - chromosome (e.g., "chr3")
column 2: start_a integer; genomic location of anchor A - start coordinate
column 3: end_a integer; genomic location of anchor A - end coordinate
column 4: chr_b character; genomic location of anchor B - chromosome (e.g., "chr3")
column 5: start_b integer; genomic location of anchor B - start coordinate
column 6: end_b integer; genomic location of anchor B - end coordinate
column 7: value numeric; p-value, FDR, or heuristic used to rank the interactions
rep2_df

data frame of observations (i.e., genomic interactions) of replicate 2, with the following columns (position of columns matter, column names are irrelevant):

column 1: chr_a character; genomic location of anchor A - chromosome (e.g., "chr3")
column 2: start_a integer; genomic location of anchor A - start coordinate
column 3: end_a integer; genomic location of anchor A - end coordinate
column 4: chr_b character; genomic location of anchor B - chromosome (e.g., "chr3")
column 5: start_b integer; genomic location of anchor B - start coordinate
column 6: end_b integer; genomic location of anchor B - end coordinate
column 7: value numeric; p-value, FDR, or heuristic used to rank the interactions
ambiguity_resolution_method

defines how ambiguous assignments (when one interaction in replicate 1 overlaps with multiple interactions in replicate 2 or vice versa) are resolved. Available methods:

"value" interactions are prioritized by ascending or descending value column (see sorting_direction), e.g., if two interactions in replicate 1 overlap with one interaction in replicate 2, the interaction from replicate 1 is chosen which has a lower (if sorting_direction is "ascending") or higher (if "descending") value
"overlap" the interaction pair is chosen which has the highest relative overlap, i.e., overlap in nucleotides of replicate 1 interaction anchor A and replicate 2 interaction anchor A, plus replicate 1 interaction anchor B and replicate 2 interaction anchor B, normalized by their lengths
"midpoint" the interaction pair is chosen which has the smallest distance between their anchor midpoints, i.e., distance from midpoint of replicate 1 interaction anchor A to midpoint of replicate 2 interaction anchor A, plus distance from midpoint of replicate 1 interaction anchor B to midpoint of replicate 2 interaction anchor B
max_gap

integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)

Value

data frame with the following columns:

column 1: rep1_idx index of interaction in replicate 1 (i.e., row index in rep1_df)
column 2: rep2_idx index of interaction in replicate 2 (i.e., row index in rep2_df)
column 3: arv ambiguity resolution value used turn m:n mapping into 1:1 mapping. Interaction pairs with lower arv are prioritized.

Examples

rep1_df <- idr2d:::chiapet$rep1_df
rep1_df$fdr <- preprocess(rep1_df$fdr, "log_additive_inverse")

rep2_df <- idr2d:::chiapet$rep2_df
rep2_df$fdr <- preprocess(rep2_df$fdr, "log_additive_inverse")

# shuffle to break preexisting order
rep1_df <- rep1_df[sample.int(nrow(rep1_df)), ]
rep2_df <- rep2_df[sample.int(nrow(rep2_df)), ]

# sort by value column
rep1_df <- dplyr::arrange(rep1_df, rep1_df$fdr)
rep2_df <- dplyr::arrange(rep2_df, rep2_df$fdr)

pairs_df <- establish_overlap2d(rep1_df, rep2_df)

Estimates IDR for Genomic Peaks or Genomic Interactions

Description

Estimates IDR for Genomic Peaks or Genomic Interactions

Usage

estimate_idr(
  rep1_df,
  rep2_df,
  analysis_type = "IDR2D",
  value_transformation = c("identity", "additive_inverse", "multiplicative_inverse",
    "log", "log_additive_inverse"),
  ambiguity_resolution_method = c("overlap", "midpoint", "value"),
  remove_nonstandard_chromosomes = TRUE,
  max_factor = 1.5,
  jitter_factor = 1e-04,
  max_gap = -1L,
  mu = 0.1,
  sigma = 1,
  rho = 0.2,
  p = 0.5,
  eps = 0.001,
  max_iteration = 30,
  local_idr = TRUE
)

Arguments

rep1_df

data frame of observations (i.e., genomic peaks or genomic interactions) of replicate 1. If analysis_type is IDR1D, the columns of rep1_df are described in establish_bijection1d, otherwise in establish_bijection2d
rep2_df

data frame of observations (i.e., genomic peaks or genomic interactions) of replicate 2. Same columns as rep1_df.
analysis_type

"IDR2D" for genomic interaction data sets, "IDR1D" for genomic peak data sets
value_transformation

the values in x have to be transformed in a way such that when ordered in descending order, more significant interactions end up on top of the list. If the values in x are p-values, "log_additive_inverse" is recommended. The following transformations are supported:

"identity" no transformation is performed on x
"additive_inverse" x. = -x
"multiplicative_inverse" x. = 1 / x
"log" x. = log(x). Note: zeros are replaced by .Machine$double.xmin
"log_additive_inverse" x. = -log(x), recommended if x are p-values. Note: zeros are replaced by .Machine$double.xmin

either "ascending" (more significant interactions have lower value in value column) or "descending" (more significant interactions have higher value in value column)
ambiguity_resolution_method

defines how ambiguous assignments (when one interaction or peak in replicate 1 overlaps with multiple interactions or peaks in replicate 2 or vice versa) are resolved. For available methods, see establish_overlap1d or establish_overlap2d, respectively.
remove_nonstandard_chromosomes

removes peaks and interactions containing genomic locations on non-standard chromosomes using keepStandardChromosomes (default is TRUE)
max_factor

numeric; controls the replacement values for Inf and -Inf. Inf are replaced by max(x) * max_factor and -Inf are replaced by min(x) / max_factor.
jitter_factor

numeric; controls the magnitude of the noise that is added to x. This is done to break ties in x. Set jitter_factor = NULL for no jitter.
max_gap

integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)
mu

a starting value for the mean of the reproducible component.
sigma

a starting value for the standard deviation of the reproducible component.
rho

a starting value for the correlation coefficient of the reproducible component.
p

a starting value for the proportion of reproducible component.
eps

Stopping criterion. Iterations stop when the increment of log-likelihood is < eps*log-likelihood, Default=0.001.
max_iteration

integer; maximum number of iterations for IDR estimation (defaults to 30)
local_idr

see est.IDR

Value

See estimate_idr1d or estimate_idr2d, respectively.

References

Q. Li, J. B. Brown, H. Huang and P. J. Bickel. (2011) Measuring reproducibility of high-throughput experiments. Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779.

Examples

idr_results <- estimate_idr(idr2d:::chiapet$rep1_df,
                            idr2d:::chiapet$rep2_df,
                            analysis_type = "IDR2D",
                            value_transformation = "log_additive_inverse")
summary(idr_results)

Estimates IDR for Genomic Peak Data

Description

This method estimates Irreproducible Discovery Rates (IDR) for peaks in replicated ChIP-seq experiments.

Usage

estimate_idr1d(
  rep1_df,
  rep2_df,
  value_transformation = c("identity", "additive_inverse", "multiplicative_inverse",
    "log", "log_additive_inverse"),
  ambiguity_resolution_method = c("overlap", "midpoint", "value"),
  remove_nonstandard_chromosomes = TRUE,
  max_factor = 1.5,
  jitter_factor = 1e-04,
  max_gap = -1L,
  mu = 0.1,
  sigma = 1,
  rho = 0.2,
  p = 0.5,
  eps = 0.001,
  max_iteration = 30,
  local_idr = TRUE
)

Arguments

rep1_df

data frame of observations (i.e., genomic peaks) of replicate 1, with at least the following columns (position of columns matter, column names are irrelevant):

column 1: chr character; genomic location of peak - chromosome (e.g., "chr3")
column 2: start integer; genomic location of peak - start coordinate
column 3: end integer; genomic location of peak - end coordinate
column 4: value numeric; p-value, FDR, or heuristic used to rank the interactions
rep2_df

data frame of observations (i.e., genomic peaks) of replicate 2, with the following columns (position of columns matter, column names are irrelevant):

column 1: chr character; genomic location of peak - chromosome (e.g., "chr3")
column 2: start integer; genomic location of peak - start coordinate
column 3: end integer; genomic location of peak - end coordinate
column 4: value numeric; p-value, FDR, or heuristic used to rank the interactions
value_transformation

the values in x have to be transformed in a way such that when ordered in descending order, more significant interactions end up on top of the list. If the values in x are p-values, "log_additive_inverse" is recommended. The following transformations are supported:

"identity" no transformation is performed on x
"additive_inverse" x. = -x
"multiplicative_inverse" x. = 1 / x
"log" x. = log(x). Note: zeros are replaced by .Machine$double.xmin
"log_additive_inverse" x. = -log(x), recommended if x are p-values. Note: zeros are replaced by .Machine$double.xmin

either "ascending" (more significant interactions have lower value in value column) or "descending" (more significant interactions have higher value in value column)
ambiguity_resolution_method

defines how ambiguous assignments (when one interaction in replicate 1 overlaps with multiple interactions in replicate 2 or vice versa) are resolved. Available methods:

"value" interactions are prioritized by ascending or descending value column (see sorting_direction), e.g., if two interactions in replicate 1 overlap with one interaction in replicate 2, the interaction from replicate 1 is chosen which has a lower (if sorting_direction is "ascending") or higher (if "descending") value
"overlap" the interaction pair is chosen which has the highest relative overlap, i.e., overlap in nucleotides of replicate 1 interaction anchor A and replicate 2 interaction anchor A, plus replicate 1 interaction anchor B and replicate 2 interaction anchor B, normalized by their lengths
"midpoint" the interaction pair is chosen which has the smallest distance between their anchor midpoints, i.e., distance from midpoint of replicate 1 interaction anchor A to midpoint of replicate 2 interaction anchor A, plus distance from midpoint of replicate 1 interaction anchor B to midpoint of replicate 2 interaction anchor B
remove_nonstandard_chromosomes

removes peaks containing genomic locations on non-standard chromosomes using keepStandardChromosomes (default is TRUE)
max_factor

numeric; controls the replacement values for Inf and -Inf. Inf are replaced by max(x) * max_factor and -Inf are replaced by min(x) / max_factor.
jitter_factor

numeric; controls the magnitude of the noise that is added to x. This is done to break ties in x. Set jitter_factor = NULL for no jitter.
max_gap

integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)
mu

a starting value for the mean of the reproducible component.
sigma

a starting value for the standard deviation of the reproducible component.
rho

a starting value for the correlation coefficient of the reproducible component.
p

a starting value for the proportion of reproducible component.
eps

Stopping criterion. Iterations stop when the increment of log-likelihood is < eps*log-likelihood, Default=0.001.
max_iteration

integer; maximum number of iterations for IDR estimation (defaults to 30)
local_idr

see est.IDR

Value

List with three components, (rep1_df, rep2_df, and analysis_type) containing the interactions from input data frames rep1_df and rep2_df with the following additional columns:

column 1: chr character; genomic location of peak - chromosome (e.g., "chr3")
column 2: start integer; genomic location of peak - start coordinate
column 3: end integer; genomic location of peak - end coordinate
column 4: value numeric; p-value, FDR, or heuristic used to rank the peaks
column 5: rep_value numeric; value of corresponding replicate peak. If no corresponding peak was found, rep_value is set to NA.
column 6: rank integer; rank of the peak, established by value column, ascending order
column 7: rep_rank integer; rank of corresponding replicate peak. If no corresponding peak was found, rep_rank is set to NA.
column 8: idx integer; peak index, primary key
column 9: rep_idx integer; specifies the index of the corresponding peak in the other replicate (foreign key). If no corresponding peak was found, rep_idx is set to NA.
column 10: idr IDR of the peak and the corresponding peak in the other replicate. If no corresponding peak was found, idr is set to NA.

References

Q. Li, J. B. Brown, H. Huang and P. J. Bickel. (2011) Measuring reproducibility of high-throughput experiments. Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779.

Examples

idr_results <- estimate_idr1d(idr2d:::chipseq$rep1_df,
                              idr2d:::chipseq$rep2_df,
                              value_transformation = "log")
summary(idr_results)

Estimates IDR for Genomic Interaction Data

Description

This method estimates Irreproducible Discovery Rates (IDR) between two replicates of experiments identifying genomic interactions, such as Hi-C, ChIA-PET, and HiChIP.

Usage

estimate_idr2d(
  rep1_df,
  rep2_df,
  value_transformation = c("identity", "additive_inverse", "multiplicative_inverse",
    "log", "log_additive_inverse"),
  ambiguity_resolution_method = c("overlap", "midpoint", "value"),
  remove_nonstandard_chromosomes = TRUE,
  max_factor = 1.5,
  jitter_factor = 1e-04,
  max_gap = -1L,
  mu = 0.1,
  sigma = 1,
  rho = 0.2,
  p = 0.5,
  eps = 0.001,
  max_iteration = 30,
  local_idr = TRUE
)

Arguments

rep1_df

data frame of observations (i.e., genomic interactions) of replicate 1, with at least the following columns (position of columns matter, column names are irrelevant):

column 1: chr_a character; genomic location of anchor A - chromosome (e.g., "chr3")
column 2: start_a integer; genomic location of anchor A - start coordinate
column 3: end_a integer; genomic location of anchor A - end coordinate
column 4: chr_b character; genomic location of anchor B - chromosome (e.g., "chr3")
column 5: start_b integer; genomic location of anchor B - start coordinate
column 6: end_b integer; genomic location of anchor B - end coordinate
column 7: value numeric; p-value, FDR, or heuristic used to rank the interactions
rep2_df

data frame of observations (i.e., genomic interactions) of replicate 2, with the following columns (position of columns matter, column names are irrelevant):

column 1: chr_a character; genomic location of anchor A - chromosome (e.g., "chr3")
column 2: start_a integer; genomic location of anchor A - start coordinate
column 3: end_a integer; genomic location of anchor A - end coordinate
column 4: chr_b character; genomic location of anchor B - chromosome (e.g., "chr3")
column 5: start_b integer; genomic location of anchor B - start coordinate
column 6: end_b integer; genomic location of anchor B - end coordinate
column 7: value numeric; p-value, FDR, or heuristic used to rank the interactions
value_transformation

the values in x have to be transformed in a way such that when ordered in descending order, more significant interactions end up on top of the list. If the values in x are p-values, "log_additive_inverse" is recommended. The following transformations are supported:

"identity" no transformation is performed on x
"additive_inverse" x. = -x
"multiplicative_inverse" x. = 1 / x
"log" x. = log(x). Note: zeros are replaced by .Machine$double.xmin
"log_additive_inverse" x. = -log(x), recommended if x are p-values. Note: zeros are replaced by .Machine$double.xmin

either "ascending" (more significant interactions have lower value in value column) or "descending" (more significant interactions have higher value in value column)
ambiguity_resolution_method

defines how ambiguous assignments (when one interaction in replicate 1 overlaps with multiple interactions in replicate 2 or vice versa) are resolved. Available methods:

"value" interactions are prioritized by ascending or descending value column (see sorting_direction), e.g., if two interactions in replicate 1 overlap with one interaction in replicate 2, the interaction from replicate 1 is chosen which has a lower (if sorting_direction is "ascending") or higher (if "descending") value
"overlap" the interaction pair is chosen which has the highest relative overlap, i.e., overlap in nucleotides of replicate 1 interaction anchor A and replicate 2 interaction anchor A, plus replicate 1 interaction anchor B and replicate 2 interaction anchor B, normalized by their lengths
"midpoint" the interaction pair is chosen which has the smallest distance between their anchor midpoints, i.e., distance from midpoint of replicate 1 interaction anchor A to midpoint of replicate 2 interaction anchor A, plus distance from midpoint of replicate 1 interaction anchor B to midpoint of replicate 2 interaction anchor B
remove_nonstandard_chromosomes

removes interactions containing genomic locations on non-standard chromosomes using keepStandardChromosomes (default is TRUE)
max_factor

numeric; controls the replacement values for Inf and -Inf. Inf are replaced by max(x) * max_factor and -Inf are replaced by min(x) / max_factor.
jitter_factor

numeric; controls the magnitude of the noise that is added to x. This is done to break ties in x. Set jitter_factor = NULL for no jitter.
max_gap

integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)
mu

a starting value for the mean of the reproducible component.
sigma

a starting value for the standard deviation of the reproducible component.
rho

a starting value for the correlation coefficient of the reproducible component.
p

a starting value for the proportion of reproducible component.
eps

Stopping criterion. Iterations stop when the increment of log-likelihood is < eps*log-likelihood, Default=0.001.
max_iteration

integer; maximum number of iterations for IDR estimation (defaults to 30)
local_idr

see est.IDR

Value

List with three components, (rep1_df, rep2_df, and analysis_type) containing the interactions from input data frames rep1_df and rep2_df with the following additional columns:

column 1: chr_a character; genomic location of anchor A - chromosome (e.g., "chr3")
column 2: start_a integer; genomic location of anchor A - start coordinate
column 3: end_a integer; genomic location of anchor A - end coordinate
column 4: chr_b character; genomic location of anchor B - chromosome (e.g., "chr3")
column 5: start_b integer; genomic location of anchor B - start coordinate
column 6: end_b integer; genomic location of anchor B - end coordinate
column 7: value numeric; p-value, FDR, or heuristic used to rank the interactions
column 8: "rep_value" numeric; value of corresponding replicate interaction. If no corresponding interaction was found, rep_value is set to NA.
column 9: "rank" integer; rank of the interaction, established by value column, ascending order
column 10: "rep_rank" integer; rank of corresponding replicate interaction. If no corresponding interaction was found, rep_rank is set to NA.
column 11: "idx" integer; interaction index, primary key
column 12: "rep_idx" integer; specifies the index of the corresponding interaction in the other replicate (foreign key). If no corresponding interaction was found, rep_idx is set to NA.
idr IDR of the interaction and the corresponding interaction in the other replicate. If no corresponding interaction was found, idr is set to NA.

References

Q. Li, J. B. Brown, H. Huang and P. J. Bickel. (2011) Measuring reproducibility of high-throughput experiments. Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779.

Examples

idr_results <- estimate_idr2d(idr2d:::chiapet$rep1_df,
                              idr2d:::chiapet$rep2_df,
                              value_transformation = "log_additive_inverse")
summary(idr_results)

Estimates IDR for Genomic Interactions measured by Hi-C experiments

Description

This method estimates Irreproducible Discovery Rates (IDR) of genomic interactions between two replicates of Hi-C experiments.

Before calling this method, call Juicer .hic contact matrix c

The contact matrix is subdivided into blocks, where the block size is determined by resolution. The reads per block are used to rank blocks and replicate blocks are easily matched by genomic location.

Usage

estimate_idr2d_hic(
  rep1_df,
  rep2_df,
  combined_min_value = 30,
  combined_max_value = Inf,
  min_value = -Inf,
  max_value = Inf,
  max_factor = 1.5,
  jitter_factor = 1e-04,
  mu = 0.1,
  sigma = 1,
  rho = 0.2,
  p = 0.5,
  eps = 0.001,
  max_iteration = 30,
  local_idr = TRUE
)

Arguments

rep1_df

data frame of either parsed .hic file from Juicer (output of parse_juicer_matrix) or parsed .matrix and .bed files from HiC-Pro (output of parse_hic_pro_matrix) for replicate 1
rep2_df

data frame of either parsed .hic file from Juicer (output of parse_juicer_matrix) or parsed .matrix and .bed files from HiC-Pro (output of parse_hic_pro_matrix) for replicate 2
combined_min_value

exclude blocks with a combined (replicate 1 + replicate 2) read count or normalized read count of less than combined_min_value (default is 20 reads, set combined_min_value = -Inf to disable)
combined_max_value

exclude blocks with a combined (replicate 1 + replicate 2) read count or normalized read count of more than combined_max_value (disabled by default, set combined_max_value = Inf to disable)
min_value

exclude blocks with a read count or normalized read count of less than min_value in one replicate (disabled by default, set min_value = -Inf to disable)
max_value

exclude blocks with a read count or normalized read count of more than max_value in one replicate (disabled by default, set max_value = Inf to disable)
max_factor

numeric; controls the replacement values for Inf and -Inf. Inf are replaced by max(x) * max_factor and -Inf are replaced by min(x) / max_factor.
jitter_factor

numeric; controls the magnitude of the noise that is added to x. This is done to break ties in x. Set jitter_factor = NULL for no jitter.
mu

a starting value for the mean of the reproducible component.
sigma

a starting value for the standard deviation of the reproducible component.
rho

a starting value for the correlation coefficient of the reproducible component.
p

a starting value for the proportion of reproducible component.
eps

Stopping criterion. Iterations stop when the increment of log-likelihood is < eps*log-likelihood, Default=0.001.
max_iteration

integer; maximum number of iterations for IDR estimation (defaults to 30)
local_idr

see est.IDR

Value

Data frame with the following columns:

column 1: interaction character; genomic location of interaction block (e.g., "chr1:204940000-204940000")
column 2: value numeric; p-value, FDR, or heuristic used to rank the interactions
column 3: "rep_value" numeric; value of corresponding replicate interaction
column 4: "rank" integer; rank of the interaction, established by value column, ascending order
column 5: "rep_rank" integer; rank of corresponding replicate interaction
column 6: "idr" integer; IDR of the block and the corresponding block in the other replicate

References

Q. Li, J. B. Brown, H. Huang and P. J. Bickel. (2011) Measuring reproducibility of high-throughput experiments. Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779.

Examples

idr_results_df <- estimate_idr2d_hic(idr2d:::hic$rep1_df,
                                     idr2d:::hic$rep2_df)
summary(idr_results_df)

Example Hi-C data set

Description

This object contains data from a Hi-C contact map of human chromosome 1 and a resolution of 2.5 * 10^6, extracted from GEO series GSE71831.

Usage

hic

Format

A list with two components, the data frames rep1_df and rep2_df, which have the following four columns:

column 1: chr character; genomic location of block - chromosome (e.g., "chr3")
column 2: region1 integer; genomic location of block - coordinate A
column 3: region2 integer; genomic location of block - coordinate B
column 4: value numeric; heuristic used to rank blocks, in this case: number of reads

Parse .matrix and .bed files from HiC-Pro for IDR2D analysis

Description

This function is used to convert the contact matrix from a HiC-Pro pipeline analysis run into an IDR2D compatible format. It takes one .matrix and one .bed file per replicate from HiC-Pro and returns the contact matrix for a specific chromosome for IDR2D analysis (see estimate_idr2d_hic)

Usage

parse_hic_pro_matrix(matrix_file, bed_file, chromosome = "chr1")

Arguments

matrix_file

path to .matrix file from HiC-Pro analysis run
bed_file

path to .bed file from HiC-Pro analysis run
chromosome

chromsome name to be analyzed, defaults to UCSC chromosome 1 ("chr1")

Value

Data frame with the following columns:

column 1: chr character; chromosome of block (e.g., "chr3")
column 2: region1 integer; genomic location of side A of block in Hi-C contact matrix
column 3: region2 integer; genomic location of side B of block in Hi-C contact matrix
column 4: value numeric; (normalized) read count in block

References

Servant, N., Varoquaux, N., Lajoie, B.R. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16, 259 (2015) doi:10.1186/s13059-015-0831-x

Parse .hic files from Juicer for IDR2D analysis

Description

parse_juicer_matrix uses the Python package hic-straw internally to read .hic contact matrix files (see hic-straw on PyPI or the Aiden lab GitHub repository for more information).

The contact matrix is subdivided into blocks, where the block size is determined by resolution. The reads per block are used to rank blocks and replicate blocks are easily matched by genomic location.

Usage

parse_juicer_matrix(
  hic_file,
  resolution = 1e+06,
  normalization = c("NONE", "VC", "VC_SQRT", "KR"),
  chromosome = "chr1",
  use_python = NULL,
  use_virtualenv = NULL,
  use_condaenv = NULL
)

Arguments

hic_file

path to .hic file (either local file path or URL).
resolution

block resolution of Hi-C contact matrix in base pairs, defaults to 1,000,000 bp (usually one of the following: 2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000)
normalization

normalization step performed by Python package hic-straw, one of the following: "NONE", "VC", "VC_SQRT", "KR".
chromosome

chromsome name to be analyzed, defaults to UCSC chromosome 1 ("chr1")
use_python

if Python is not on PATH, specify path to Python binary here (see use_python)
use_virtualenv

if Python package hic-straw is not in base virtualenv environment, specify environment here (see use_virtualenv)
use_condaenv

if Python package hic-straw is not in base conda environment, specify environment here (see use_condaenv)

Value

Data frame with the following columns:

column 1: chr character; chromosome of block (e.g., "chr3")
column 2: region1 integer; genomic location of side A of block in Hi-C contact matrix
column 3: region2 integer; genomic location of side B of block in Hi-C contact matrix
column 4: value numeric; (normalized) read count in block

References

Neva C. Durand, James T. Robinson, Muhammad S. Shamim, Ido Machol, Jill P. Mesirov, Eric S. Lander, and Erez Lieberman Aiden. "Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom." Cell Systems 3(1), 2016.

Prepares Data for IDR Analysis

Description

This method removes invalid values, establishes the correct ranking, and breaks ties prior to IDR analysis.

Inf and -Inf are replaced by max(x) * max_factor and min(x) / max_factor, respectively.

NA values in x are replaced by mean(x).

All values in x are transformed using the transformation specified in value_transformation.

Lastly, a small amount of noise is added to x to break ties. The magnitude of the noise is controlled by jitter_factor.

Usage

preprocess(
  x,
  value_transformation = c("identity", "additive_inverse", "multiplicative_inverse",
    "log", "log_additive_inverse"),
  max_factor = 1.5,
  jitter_factor = 1e-04
)

Arguments

x

numeric vector of values
value_transformation

the values in x have to be transformed in a way such that when ordered in descending order, more significant interactions end up on top of the list. If the values in x are p-values, "log_additive_inverse" is recommended. The following transformations are supported:

"identity" no transformation is performed on x
"additive_inverse" x. = -x
"multiplicative_inverse" x. = 1 / x
"log" x. = log(x). Note: zeros are replaced by .Machine$double.xmin
"log_additive_inverse" x. = -log(x), recommended if x are p-values. Note: zeros are replaced by .Machine$double.xmin

either "ascending" (more significant interactions have lower value in value column) or "descending" (more significant interactions have higher value in value column)
max_factor

numeric; controls the replacement values for Inf and -Inf. Inf are replaced by max(x) * max_factor and -Inf are replaced by min(x) / max_factor.
jitter_factor

numeric; controls the magnitude of the noise that is added to x. This is done to break ties in x. Set jitter_factor = NULL for no jitter.

Value

numeric vector; transformed and stripped values of x, ready for IDR analysis

Examples

rep1_df <- idr2d:::chiapet$rep1_df
rep1_df$fdr <- preprocess(rep1_df$fdr, "log_additive_inverse")

Removes Peaks on Non-standard Chromosomes

Description

Removes Peaks on Non-standard Chromosomes

Usage

remove_nonstandard_chromosomes1d(x)

Arguments

x

data frame of genomic peaks, with the following columns (position of columns matter, column names are irrelevant):

column 1: chr character; genomic location of peak - chromosome (e.g., "chr3")
column 2: start integer; genomic location of peak - start coordinate
column 3: end integer; genomic location of peak - end coordinate
column 4: value numeric; p-value, FDR, or heuristic used to rank the peaks

Value

x without non-standard chromosomes.

Examples

rep1_df <- remove_nonstandard_chromosomes1d(idr2d:::chipseq$rep1_df)

Removes Interactions on Non-standard Chromosomes

Description

Removes Interactions on Non-standard Chromosomes

Usage

remove_nonstandard_chromosomes2d(x)

Arguments

x

data frame of genomic interactions, with the following columns (position of columns matter, column names are irrelevant):

column 1: chr_a character; genomic location of anchor A - chromosome (e.g., "chr3")
column 2: start_a integer; genomic location of anchor A - start coordinate
column 3: end_a integer; genomic location of anchor A - end coordinate
column 4: chr_b character; genomic location of anchor B - chromosome (e.g., "chr3")
column 5: start_b integer; genomic location of anchor B - start coordinate
column 6: end_b integer; genomic location of anchor B - end coordinate
column 7: value numeric; p-value, FDR, or heuristic used to rank the interactions

Value

x without non-standard chromosomes.

Examples

rep1_df <- remove_nonstandard_chromosomes2d(idr2d:::chiapet$rep1_df)