Package 'HiCaptuRe'

Annotates HiCaptuRe object from load_interactions

Description

This function annotate a HiCaptuRe object from load_interactions, based on a given annotations file

Usage

annotate_interactions(interactions, annotation, ...)

Arguments

interactions	HiCaptuRe object from load_interactions
annotation	full path to annotations file or a dataframe with 5 columns: chr, start, end, fragmentID, annotation
...	additional parameters for fread

Value

HiCaptuRe object annotated, with columns bait_1 and bait_2 substituted based on the given annotation

Examples

annotation <- system.file("extdata", "annotation_example.txt", package = "HiCaptuRe")
ibed1 <- system.file("extdata", "ibed1_example.zip", package = "HiCaptuRe")
interactions <- load_interactions(ibed1, select_chr = "19")
interactions <- annotate_interactions(interactions = interactions, annotation = annotation)

---

Digest genome for a specific restriction enzyme

Description

This function takes a genome installed and generates its digest for a given restriction enzyme

Usage

digest_genome(
  genome = "GRCh38",
  RE_name = "HindIII",
  motif = NULL,
  cut_position = NULL,
  select_chr = c(seq_len(22), "X", "Y"),
  PAR_mask = TRUE,
  PAR_file = NULL,
  ...
)

Arguments

genome	character with the name of the genome version
RE_name	name of the restriction enzyme
motif	recognition motif of the restriction enzyme
cut_position	cut position of the restriction enzyme inside the motif
select_chr	a character vector containing the specific chromosomes to used from this genome, if NULL all chromosomes will be used
PAR_mask	a logical value where the Y chromosome should exclude the Pseudoautosomical Regions (PAR) or not
PAR_file	a full path to a file containing the coordinates of Y chromosome PAR with at least 3 columns with header: seqnames, start, end
...	extra arguments for read.table

Value

list object with 2 elements: a dataframe with the digested genome, and a the parameters used for the digestion.

Note

The package provides for a PAR coordinates file only for Homo sapiens for the genome version 38

The package provides the motives and cut positions for several restriction enzymes (HindIII, MboI, DpnII, EcoRI, BamHI)

Examples

digest <- digest_genome(genome = "GRCh38", RE_name = "HindIII", select_chr = "19")

---

Computes the number of interactions by distance

Description

This function computes the number of interactions by distance for a given GenomicInteractions object

Usage

distance_summary(interactions, breaks = seq(0, 10^6, 10^5), sample = "sample")

Arguments

interactions	GenomicInteractions object from load_interactions
breaks	vector with breaks for split distances
sample	character variable with the name of the sample

Value

list with 2 tables: short_int_dist_table and long_int_dist_table, with the number of short interactions and long interactions respectively

Examples

ibed1 <- system.file("extdata", "ibed1_example.zip", package = "HiCaptuRe")
interactions1 <- load_interactions(ibed1, select_chr = "19")
df <- distance_summary(interactions = interactions1)

---

Export interactions in the desired output format

Description

This function exports interactions in different formats

Usage

export_interactions(
  interactions,
  file,
  format = "ibed",
  over.write = FALSE,
  cutoff = 5,
  parameters = FALSE
)

Arguments

interactions	GenomicInteractions object from load_interactions
file	full path to desired output file (ibed, peakmatrix, washU, washUold, cytoscape, bedpe)
format	type of output format (ibed, peakmatrix, washU, washUold, cytoscape, bedpe, seqmonk)
over.write	TRUE/FALSE to over write the output file
cutoff	Chicago score cutoff to export interactions
parameters	TRUE/FALSE to also export the parameters of the given object

Value

tibble object with the ibed table and save it in the desired output file

Examples

ibed1 <- system.file("extdata", "ibed1_example.zip", package = "HiCaptuRe")
interactions <- load_interactions(ibed1, select_chr = "19")
export_interactions(interactions = interactions, file = tempfile(), format = "ibed", over.write = TRUE)

---

Internal functions to access data held in a HiCaptuRe object.

Description

Use these functions to access data stored in each of the slots of a HiCapture object.

Usage

getParameters(x)

## S4 method for signature 'HiCaptuRe'
getParameters(x)

getByBaits(x)

## S4 method for signature 'HiCaptuRe'
getByBaits(x)

getByRegions(x)

## S4 method for signature 'HiCaptuRe'
getByRegions(x)

Arguments

x	A HiCaptuRe object

Value

getParameters(x)

A named list of named vectors with all parameters used.

getByBaits(x)

A list of tibbles with bait‑centric summaries.

getByRegions(x)

A list of 'GRanges' with region‑centric summaries.

Examples

ibed1 <- system.file("extdata", "ibed1_example.zip", package = "HiCaptuRe")
interactions <- load_interactions(ibed1, select_chr = "19")
getParameters(interactions)

baits <- c("ENST00000332235", "ENST00000516525")
interactions_baits <- interactionsByBaits(interactions = interactions, baits = baits)
getByBaits(interactions_baits)

regions <- GenomicRanges::GRanges(seqnames = 19, ranges = IRanges::IRanges(start = c(500000, 1000000), end = c(510000, 1100000)))
interactions_regions <- interactionsByRegions(interactions = interactions, regions = regions)
getByRegions(interactions_regions)

---

HiCaptuRe Class

Description

A S4 class to represent interactions between genomic regions

Slots

parameters

List of parameters used to create the object and subsequence analysis

ByBaits

List of Baits used by interactionsByBaits.

ByRegions

List of Regions used by interactionsByRegions

Note

This class contains a GenomicInteractions object inside therefore all methods available to it can be used. This type of object should be created through the function load_interactions

---

Filters HiCaptuRe object by baits

Description

This function filters a HiCaptuRe object from load_interactions by a set of given bait(s)

Usage

interactionsByBaits(interactions, baits, sep = ",", invert = FALSE)

Arguments

interactions	a HiCaptuRe object
baits	character vector containing bait names
sep	character separating baits names when several baits in same fragment
invert	TRUE/FALSE if need those interactions that do NOT contain the given baits

Value

The returned object includes a filtered set of interactions and updates the ByBaits slot with a tibble summarizing bait-wise interaction statistics (number of interactions, other ends, etc.). Baits that are not present in the interaction data will have empty statistics.

Examples

ibed1 <- system.file("extdata", "ibed1_example.zip", package = "HiCaptuRe")
interactions <- load_interactions(ibed1, select_chr = "19")
baits <- c("ENST00000332235", "ENST00000516525")
interactions_baits <- interactionsByBaits(interactions = interactions, baits = baits)

---

Filters HiCaptuRe object by overlaping regions

Description

This function filters a HiCaptuRe object from load_interactions by overlaping regions

Usage

interactionsByRegions(
  interactions,
  regions,
  chr = NULL,
  start = NULL,
  end = NULL,
  invert = FALSE
)

Arguments

interactions	HiCaptuRe object
regions	full path to regions file (bed format) or a GRanges object
chr	column name of chromosome values
start	column name of start positions
end	column name of end positions
invert	TRUE/FALSE if need those interactions that do NOT overlaps with any regions

Value

HiCaptuRe object filtered by regions, by default with additional columns regarding overlap on each node. If invert=T no additional columns. And an additional slot ByRegions with region-centric statistics

Examples

ibed1 <- system.file("extdata", "ibed1_example.zip", package = "HiCaptuRe")
interactions <- load_interactions(ibed1, select_chr = "19")
regions <- GenomicRanges::GRanges(seqnames = 19, ranges = IRanges::IRanges(start = c(500000, 1000000), end = c(510000, 1100000)))
interactions_regions <- interactionsByRegions(interactions = interactions, regions = regions)

---

Computes the intersect between a list of interactions objects

Description

This function computes all the possible intersects for a given list of HiCaptuRe objects

Usage

intersect_interactions(interactions_list, distance.boxplot = FALSE, ...)

Arguments

interactions_list	list of HiCaptuRe objects from load_interactions
distance.boxplot	logical, by default FALSE, plot a boxplot of log10 distance of each intersection in the upset plot
...	extra arguments for UpSetR

Value

A list with:

intersections

A named list of intersected HiCaptuRe objects

upset

An UpSetR plot

venn

A ggVennDiagram plot (NULL if > 7 sets)

Examples

ibed1 <- system.file("extdata", "ibed1_example.zip", package = "HiCaptuRe")
interactions1 <- load_interactions(ibed1, select_chr = "19")
ibed2 <- system.file("extdata", "ibed2_example.zip", package = "HiCaptuRe")
interactions2 <- load_interactions(ibed2, select_chr = "19")
interactions_list <- list(ibed1 = interactions1, ibed2 = interactions2)
intersection <- intersect_interactions(interactions_list = interactions_list)

---

Loads interaction file into GenomicInteractions Object

Description

This function loads interaction files from Chicago R package into a GenomicInteractions Object, and remove possible duplicated interactions

Usage

load_interactions(file, sep = "\t", ...)

Arguments

file	full path to the interaction file (seqmonk, ibed, washU)
sep	separator to read the file
...	arguments to pass to digest_genome

Value

HiCaptuRe object

Examples

ibed1 <- system.file("extdata", "ibed1_example.zip", package = "HiCaptuRe")
interactions <- load_interactions(ibed1, select_chr = "19")

---

Creates a list of HiCaptuRe objects based on a peakmatrix

Description

This function creates a list of HiCaptuRe objects separating all the samples included on a peakmatrix.

Usage

peakmatrix2list(peakmatrix, cutoff = 5)

Arguments

peakmatrix	HiCaptuRe object of a peakmatrix
cutoff	Chicago score cut-off to filter interactions

Value

A named list of HiCaptuRe objects, each corresponding to a sample (inferred from CS_* columns in the peakmatrix).

Examples

peakmatrix <- system.file("extdata", "peakmatrix_example.zip", package = "HiCaptuRe")
interactions <- load_interactions(peakmatrix, select_chr = "19")
interactions_list <- peakmatrix2list(peakmatrix = interactions)

---

Generate the plot based on distance output

Description

This function plots the distances by different approaches for the output of distance_summary

Usage

plot_distance_summary(distances, type_of_value = "absolute")

Arguments

distances	dataframes output from distance_summary
type_of_value	an element from: absolute, by_int_type, by_total

Details

The type_of_value argument could be: Absolute: plots the Absolute number of interactions. By_int_type: plots the number of interactions divided by the total number of interactions of each type. By_total: plots the number of interactions divided by the total number of interactions

Value

list with the plots

Examples

ibed1 <- system.file("extdata", "ibed1_example.zip", package = "HiCaptuRe")
interactions1 <- load_interactions(ibed1, select_chr = "19")
df <- distance_summary(interactions = interactions1)
plots <- plot_distance_summary(distances = df)

---