Package 'ChIPseeker'

Title: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
Description: This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.
Authors: Guangchuang Yu [aut, cre] , Ming Li [ctb], Qianwen Wang [ctb], Yun Yan [ctb], Hervé Pagès [ctb], Michael Kluge [ctb], Thomas Schwarzl [ctb], Zhougeng Xu [ctb], Chun-Hui Gao [ctb]
Maintainer: Guangchuang Yu <[email protected]>
License: Artistic-2.0
Version: 1.43.0
Built: 2024-10-30 04:45:22 UTC
Source: https://github.com/bioc/ChIPseeker

Help Index


.

Description

capture name of variable

Usage

.(..., .env = parent.frame())

Arguments

...

expression

.env

environment

Value

expression

Examples

x <- 1
eval(.(x)[[1]])

annotatePeak

Description

Annotate peaks

Usage

annotatePeak(
  peak,
  tssRegion = c(-3000, 3000),
  TxDb = NULL,
  level = "transcript",
  assignGenomicAnnotation = TRUE,
  genomicAnnotationPriority = c("Promoter", "5UTR", "3UTR", "Exon", "Intron",
    "Downstream", "Intergenic"),
  annoDb = NULL,
  addFlankGeneInfo = FALSE,
  flankDistance = 5000,
  sameStrand = FALSE,
  ignoreOverlap = FALSE,
  ignoreUpstream = FALSE,
  ignoreDownstream = FALSE,
  overlap = "TSS",
  verbose = TRUE,
  columns = c("ENTREZID", "ENSEMBL", "SYMBOL", "GENENAME")
)

Arguments

peak

peak file or GRanges object

tssRegion

Region Range of TSS

TxDb

TxDb or EnsDb annotation object

level

one of transcript and gene

assignGenomicAnnotation

logical, assign peak genomic annotation or not

genomicAnnotationPriority

genomic annotation priority

annoDb

annotation package

addFlankGeneInfo

logical, add flanking gene information from the peaks

flankDistance

distance of flanking sequence

sameStrand

logical, whether find nearest/overlap gene in the same strand

ignoreOverlap

logical, whether ignore overlap of TSS with peak

ignoreUpstream

logical, if True only annotate gene at the 3' of the peak.

ignoreDownstream

logical, if True only annotate gene at the 5' of the peak.

overlap

one of 'TSS' or 'all', if overlap="all", then gene overlap with peak will be reported as nearest gene, no matter the overlap is at TSS region or not.

verbose

print message or not

columns

names of columns to be obtained from database

Value

data.frame or GRanges object with columns of:

all columns provided by input.

annotation: genomic feature of the peak, for instance if the peak is located in 5'UTR, it will annotated by 5'UTR. Possible annotation is Promoter-TSS, Exon, 5' UTR, 3' UTR, Intron, and Intergenic.

geneChr: Chromosome of the nearest gene

geneStart: gene start

geneEnd: gene end

geneLength: gene length

geneStrand: gene strand

geneId: entrezgene ID

distanceToTSS: distance from peak to gene TSS

if annoDb is provided, extra column will be included:

ENSEMBL: ensembl ID of the nearest gene

SYMBOL: gene symbol

GENENAME: full gene name

Author(s)

G Yu

See Also

plotAnnoBar plotAnnoPie plotDistToTSS

Examples

## Not run: 
require(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
peakfile <- system.file("extdata", "sample_peaks.txt", package="ChIPseeker")
peakAnno <- annotatePeak(peakfile, tssRegion=c(-3000, 3000), TxDb=txdb)
peakAnno

## End(Not run)

as.data.frame.csAnno

Description

convert csAnno object to data.frame

Usage

## S3 method for class 'csAnno'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

Arguments

x

csAnno object

row.names

row names

optional

should be omitted.

...

additional parameters

Value

data.frame

Author(s)

Guangchuang Yu https://guangchuangyu.github.io


as.GRanges

Description

convert csAnno object to GRanges

Usage

as.GRanges(x)

Arguments

x

csAnno object

Value

GRanges object

Author(s)

Guangchuang Yu https://guangchuangyu.github.io


check upstream and downstream parameter

Description

check_upstream_and_downstream

Usage

check_upstream_and_downstream(upstream, downstream)

Arguments

upstream

upstream

downstream

downstream


combine_csAnno

Description

Combine csAnno Object

Usage

combine_csAnno(x, ...)

Arguments

x

csAnno object

...

csAnno objects

Details

https://github.com/YuLab-SMU/ChIPseeker/issues/157

Value

csAnno object


covplot

Description

plot peak coverage

Usage

covplot(
  peak,
  weightCol = NULL,
  xlab = "Chromosome Size (bp)",
  ylab = "",
  title = "ChIP Peaks over Chromosomes",
  chrs = NULL,
  xlim = NULL,
  lower = 1,
  fill_color = "black"
)

Arguments

peak

peak file or GRanges object

weightCol

weight column of peak

xlab

xlab

ylab

ylab

title

title

chrs

selected chromosomes to plot, all chromosomes by default

xlim

ranges to plot, default is whole chromosome

lower

lower cutoff of coverage signal

fill_color

specify the color/palette for the plot. Order matters

Value

ggplot2 object

Author(s)

G Yu


Class "csAnno" This class represents the output of ChIPseeker Annotation

Description

Class "csAnno" This class represents the output of ChIPseeker Annotation

Slots

anno

annotation

tssRegion

TSS region

level

transcript or gene

hasGenomicAnnotation

logical

detailGenomicAnnotation

Genomic Annotation in detail

annoStat

annotation statistics

peakNum

number of peaks

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

See Also

annotatePeak


downloadGEObedFiles

Description

download all BED files of a particular genome version

Usage

downloadGEObedFiles(genome, destDir = getwd())

Arguments

genome

genome version

destDir

destination folder

Author(s)

G Yu


downloadGSMbedFiles

Description

download BED supplementary files of a list of GSM accession numbers

Usage

downloadGSMbedFiles(GSM, destDir = getwd())

Arguments

GSM

GSM accession numbers

destDir

destination folder

Author(s)

G Yu


dropAnno

Description

dropAnno

Usage

dropAnno(csAnno, distanceToTSS_cutoff = 10000)

Arguments

csAnno

output of annotatePeak

distanceToTSS_cutoff

distance to TSS cutoff

Details

drop annotation exceeding distanceToTSS_cutoff

Value

csAnno object

Author(s)

Guangchuang Yu


enrichAnnoOverlap

Description

calcuate overlap significant of ChIP experiments based on their nearest gene annotation

Usage

enrichAnnoOverlap(
  queryPeak,
  targetPeak,
  TxDb = NULL,
  pAdjustMethod = "BH",
  chainFile = NULL,
  distanceToTSS_cutoff = NULL
)

Arguments

queryPeak

query bed file

targetPeak

target bed file(s) or folder containing bed files

TxDb

TxDb

pAdjustMethod

pvalue adjustment method

chainFile

chain file for liftOver

distanceToTSS_cutoff

restrict nearest gene annotation by distance cutoff

Value

data.frame

Author(s)

G Yu


enrichPeakOverlap

Description

calculate overlap significant of ChIP experiments based on the genome coordinations

Usage

enrichPeakOverlap(
  queryPeak,
  targetPeak,
  TxDb = NULL,
  pAdjustMethod = "BH",
  nShuffle = 1000,
  chainFile = NULL,
  pool = TRUE,
  mc.cores = detectCores() - 1,
  verbose = TRUE
)

Arguments

queryPeak

query bed file or GRanges object

targetPeak

target bed file(s) or folder that containing bed files or a list of GRanges objects

TxDb

TxDb

pAdjustMethod

pvalue adjustment method

nShuffle

shuffle numbers

chainFile

chain file for liftOver

pool

logical, whether pool target peaks

mc.cores

number of cores, see mclapply

verbose

logical

Value

data.frame

Author(s)

G Yu


getAnnoStat

Description

getting status of annotation

Usage

getAnnoStat(x)

Arguments

x

csAnno object


getBioRegion

Description

prepare a bioregion of selected feature

Usage

getBioRegion(
  TxDb = NULL,
  upstream = 1000,
  downstream = 1000,
  by = "gene",
  type = "start_site"
)

Arguments

TxDb

TxDb

upstream

upstream from start site or end site

downstream

downstream from start site or end site

by

one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'

type

one of "start_site", "end_site", "body"

Details

this function combined previous functions getPromoters(), getBioRegion() and getGeneBody() in order to solve the following issues.

(1) https://github.com/GuangchuangYu/ChIPseeker/issues/16

(2) https://github.com/GuangchuangYu/ChIPseeker/issues/87

The getBioRegion() function can prevoid a region of interest from txdb object. There are three kinds of regions, start_site, end_site and body.

We take transcript region to expain the differences of these three regions. tx: chr1 1000 1400.

body region refers to the 1000-1400bp.

start_site region with upstream = 100, downstream = 100 refers to 900-1100bp.

end_site region with upstream = 100, downstream = 100 refers to 1300-1500bp.

Value

GRanges object

Author(s)

Guangchuang Yu, Ming L


getGeneAnno

Description

get gene annotation, symbol, gene name etc.

Usage

getGeneAnno(annoDb, geneID, type, columns)

Arguments

annoDb

annotation package

geneID

query geneID

type

gene ID type

columns

names of columns to be obtained from database

Value

data.frame

Author(s)

G Yu


getGenomicAnnotation

Description

get Genomic Annotation of peaks

Usage

getGenomicAnnotation(
  peaks,
  distance,
  tssRegion = c(-3000, 3000),
  TxDb,
  level,
  genomicAnnotationPriority,
  sameStrand = FALSE
)

Arguments

peaks

peaks in GRanges object

distance

distance of peak to TSS

tssRegion

tssRegion, default is -3kb to +3kb

TxDb

TxDb object

level

one of gene or transcript

genomicAnnotationPriority

genomic Annotation Priority

sameStrand

whether annotate gene in same strand

Value

character vector

Author(s)

G Yu


getGEOgenomeVersion

Description

get genome version statistics collecting from GEO ChIPseq data

Usage

getGEOgenomeVersion()

Value

data.frame

Author(s)

G Yu


getGEOInfo

Description

get subset of GEO information by genome version keyword

Usage

getGEOInfo(genome, simplify = TRUE)

Arguments

genome

genome version

simplify

simplify result or not

Value

data.frame

Author(s)

G Yu


getGEOspecies

Description

accessing species statistics collecting from GEO database

Usage

getGEOspecies()

Value

data.frame

Author(s)

G Yu


getNearestFeatureIndicesAndDistances

Description

get index of features that closest to peak and calculate distance

Usage

getNearestFeatureIndicesAndDistances(
  peaks,
  features,
  sameStrand = FALSE,
  ignoreOverlap = FALSE,
  ignoreUpstream = FALSE,
  ignoreDownstream = FALSE,
  overlap = "TSS"
)

Arguments

peaks

peak in GRanges

features

features in GRanges

sameStrand

logical, whether find nearest gene in the same strand

ignoreOverlap

logical, whether ignore overlap of TSS with peak

ignoreUpstream

logical, if True only annotate gene at the 3' of the peak.

ignoreDownstream

logical, if True only annotate gene at the 5' of the peak.

overlap

one of "TSS" or "all"

Value

list

Author(s)

G Yu


getPromoters

Description

prepare the promoter regions

Usage

getPromoters(TxDb = NULL, upstream = 1000, downstream = 1000, by = "gene")

Arguments

TxDb

TxDb

upstream

upstream from TSS site

downstream

downstream from TSS site

by

one of gene or transcript

Value

GRanges object


getSampleFiles

Description

get filenames of sample files

Usage

getSampleFiles()

Value

list of file names

Author(s)

G Yu


getTagMatrix

Description

calculate the tag matrix

Usage

getTagMatrix(
  peak,
  upstream,
  downstream,
  windows,
  type,
  by,
  TxDb = NULL,
  weightCol = NULL,
  nbin = NULL,
  verbose = TRUE,
  ignore_strand = FALSE
)

Arguments

peak

peak peak file or GRanges object

upstream

the distance of upstream extension

downstream

the distance of downstream extension

windows

a collection of region

type

one of "start_site", "end_site", "body"

by

one of 'gene', 'transcript', 'exon', 'intron', '3UTR' , '5UTR', or specified by users

TxDb

TxDb or self-made granges object, served as txdb

weightCol

column name of weight, default is NULL

nbin

the amount of nbines

verbose

print message or not

ignore_strand

ignore the strand information or not

Details

getTagMatrix() function can produce the matrix for visualization. peak stands for the peak file. window stands for a collection of regions that users want to look into. Users can use window to capture the peak of interest. There are two ways to input window.

The first way is that users can use getPromoters()/getBioRegion()/makeBioRegionFromGranges() to get window and put it into getTagMatrix().

The second way is that users can use getTagMatrix() to call getPromoters()/getBioRegion()/makeBioRegionFromGranges(). In this way users do not need to input window parameter but they need to input txdb.

txdb is a set of packages contained annotation of regions of different genomes. Users can get the regions of interest through specific functions. These specific functions are built in getPromoters()/getBioRegion(). Many regions can not be gain through txdb, like insulator and enhancer regions. Users can provide these regions in the form of granges object. These self-made granges object will be passed to TxDb parameter and they will be passed to makeBioRegionFromGranges() to produce the window. In a word, TxDb parameter is a reference information. Users can pass txdb object or self-made granges into it.

Details see getPromoters,getBioRegion and makeBioRegionFromGranges

upstream and downstream parameter have different usages:

(1) window parameter is provided,

if type == 'body', upstream and downstream can use to extend the flank of body region.

if type == 'start_site'/'end_site', upstream and downstream do not play a role in getTagMatrix() function.

(2) window parameter is missing,

if type == 'body', upstream and downstream can use to extend the flank of body region.

if type == 'start_site'/'end_site', upstream and downstream refer to the upstream and downstream of the start_site or the end_site.

weightCol refers to column in peak file. This column acts as a weight vaule. Details see https://github.com/YuLab-SMU/ChIPseeker/issues/15

nbin refers to the number of bins. getTagMatrix() provide a binning method to get the tag matrix.

Value

tagMatrix


getTagMatrix.binning.internal

Description

calculate the tagMatrix by binning the idea was derived from the function of deeptools https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html

Usage

getTagMatrix.binning.internal(
  peak,
  weightCol = NULL,
  windows,
  nbin = 800,
  upstream = NULL,
  downstream = NULL,
  ignore_strand = FALSE
)

Arguments

peak

peak peak file or GRanges object

weightCol

weightCol column name of weight, default is NULL

windows

windows a collection of region with equal or not equal size, eg. promoter region, gene region.

nbin

the amount of nbines needed to be splited and it should not be more than min_body_length

upstream

rel object, NULL or actual number

downstream

rel object, NULL or actual number

ignore_strand

ignore the strand information or not

Value

tagMatrix


getTagMatrix.internal

Description

calculate the tag matrix

Usage

getTagMatrix.internal(peak, weightCol = NULL, windows, ignore_strand = FALSE)

Arguments

peak

peak file or GRanges object

weightCol

column name of weight, default is NULL

windows

a collection of region with equal size, eg. promoter region.

ignore_strand

ignore the strand information or not

Value

tagMatrix

Author(s)

G Yu


getTagMatrix2

Description

Nested function for getTagMatrix() to deal with multiple windows

Usage

getTagMatrix2(
  peak,
  upstream,
  downstream,
  windows_name,
  type,
  by,
  TxDb = NULL,
  weightCol = NULL,
  nbin = NULL,
  verbose = TRUE,
  ignore_strand = FALSE
)

Arguments

peak

peak peak file or GRanges object

upstream

the distance of upstream extension

downstream

the distance of downstream extension

windows_name

the names of windows

type

one of "start_site", "end_site", "body"

by

one of 'gene', 'transcript', 'exon', 'intron', '3UTR' , '5UTR', or specified by users

TxDb

TxDb or self-made granges object, served as txdb

weightCol

column name of weight, default is NULL

nbin

the amount of nbines

verbose

print message or not

ignore_strand

ignore the strand information or not

Details

This is an internal function.

Value

tagMatrix


internal function

Description

internal function

Usage

getTagMatrix2.binning.internal(
  peak,
  weightCol = NULL,
  windows,
  windows_name,
  nbin = 800,
  upstream = NULL,
  downstream = NULL,
  ignore_strand = FALSE
)

Arguments

peak

peak peak file or GRanges object

weightCol

column name of weight, default is NULL

windows

a collection of region

windows_name

the name of windows

nbin

the amount of nbines

upstream

the distance of upstream extension

downstream

the distance of downstream extension

ignore_strand

ignore the strand information or not


getTagMatrix2.internal

Description

getTagMatrix2.internal

Usage

getTagMatrix2.internal(
  peak,
  weightCol = NULL,
  windows,
  windows_name,
  ignore_strand = FALSE
)

Arguments

peak

peak peak file or GRanges object

weightCol

column name of weight, default is NULL

windows

a collection of region

windows_name

the name of windows

ignore_strand

ignore the strand information or not


Information Datasets

Description

ucsc genome version, precalcuated data and gsm information


makeBioRegionFromGranges

Description

make windows from granges object

Usage

makeBioRegionFromGranges(gr, by, type, upstream = 1000, downstream = 1000)

Arguments

gr

a grange object contain region of interest

by

specify be users, e.g. gene, insulator, enhancer

type

one of "start_site", "end_site", "body"

upstream

upstream from start site or end site, can be NULL if the type == 'body'

downstream

downstream from start site or end site, can be NULL if the type == 'body'

Details

makeBioRegionFromGranges() function can make bioregion from granges object.

The differences between makeBioRegionFromGranges() and getBioRegion() is that getBioRegion() get the region object from txdb object but makeBioRegionFromGranges() get the region from the granges object provided by users. For example, txdb object do not contain insulator or enhancer regions. Users can provide these regions through self-made granges object

There are three kinds of regions, start_site, end_site and body.

We take enhancer region to explain the differences of these three regions. enhancer: chr1 1000 1400.

body region refers to the 1000-1400bp.

start_site region with upstream = 100, downstream = 100 refers to 900-1100bp.

end_site region with upstream = 100, downstream = 100 refers to 1300-1500bp.

In makeBioRegionFromGranges(), upstream and downstream can be NULL if the type == 'body'. by should be specified by users and can not be omitted. by parameter will be used to made labels. type should also be specified.

https://github.com/YuLab-SMU/ChIPseeker/issues/189

Value

GRanges object


overlap

Description

calculate the overlap matrix, which is useful for vennplot

Usage

overlap(Sets)

Arguments

Sets

a list of objects

Value

data.frame

Author(s)

G Yu


peak_Profile_Heatmap

Description

plot peak heatmap and profile in a picture

Usage

peak_Profile_Heatmap(
  peak,
  weightCol = NULL,
  TxDb = NULL,
  upstream = 1000,
  downstream = 1000,
  xlab = "",
  ylab = "",
  title = NULL,
  palette = NULL,
  verbose = TRUE,
  by = "gene",
  type = "start_site",
  nbin = NULL,
  ignore_strand = FALSE,
  windows_name = NULL,
  ncol = NULL,
  nrow = NULL,
  facet_label_text_size = 12,
  conf,
  facet = "row",
  free_y = TRUE,
  height_proportion = 4
)

Arguments

peak

peak file or GRanges object

weightCol

column name of weight

TxDb

TxDb object

upstream

upstream position

downstream

downstream position

xlab

xlab

ylab

ylab

title

title

palette

palette to be filled in,details see scale_colour_brewer

verbose

print message or not

by

one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'

type

one of "start_site", "end_site", "body"

nbin

the amount of nbines

ignore_strand

ignore the strand information or not

windows_name

the name for each window, which will also be showed in the picture as labels

ncol

the ncol of plotting a list of peak

nrow

the nrow of plotting a list of peak

facet_label_text_size

the size of facet label text

conf

confidence interval

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

height_proportion

the proportion of profiling picture and heatmap


peakHeatmap

Description

plot the heatmap of peaks

Usage

peakHeatmap(
  peak,
  weightCol = NULL,
  TxDb = NULL,
  upstream = 1000,
  downstream = 1000,
  xlab = "",
  ylab = "",
  title = NULL,
  palette = NULL,
  verbose = TRUE,
  by = "gene",
  type = "start_site",
  nbin = NULL,
  ignore_strand = FALSE,
  windows,
  ncol = NULL,
  nrow = NULL
)

Arguments

peak

peak file or GRanges object

weightCol

column name of weight

TxDb

TxDb object

upstream

upstream position

downstream

downstream position

xlab

xlab

ylab

ylab

title

title

palette

palette to be filled in,details see scale_colour_brewer

verbose

print message or not

by

one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'

type

one of "start_site", "end_site", "body"

nbin

the amount of nbines

ignore_strand

ignore the strand information or not

windows

a collection of region

ncol

the ncol of plotting a list of peak

nrow

the nrow of plotting a list of peak

Value

figure

Author(s)

G Yu


peakHeatmap

Description

plot the heatmap of peaks align to a sets of regions

Usage

peakHeatmap_multiple_Sets(
  peak,
  weightCol = NULL,
  TxDb = NULL,
  upstream = 1000,
  downstream = 1000,
  xlab = "",
  ylab = "",
  title = NULL,
  palette = NULL,
  verbose = TRUE,
  by = "gene",
  type = "start_site",
  nbin = NULL,
  ignore_strand = FALSE,
  windows_name = NULL,
  ncol = NULL,
  nrow = NULL,
  facet_label_text_size = 12
)

Arguments

peak

peak file or GRanges object

weightCol

column name of weight

TxDb

TxDb object

upstream

upstream position

downstream

downstream position

xlab

xlab

ylab

ylab

title

title

palette

palette to be filled in,details see scale_colour_brewer

verbose

print message or not

by

one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'

type

one of "start_site", "end_site", "body"

nbin

the amount of nbines

ignore_strand

ignore the strand information or not

windows_name

the name for each window, which will also be showed in the picture as labels

ncol

the ncol of plotting a list of peak

nrow

the nrow of plotting a list of peak

facet_label_text_size

the size of facet label text

Value

figure


plotAnnoBar method generics

Description

plotAnnoBar method for csAnno instance

Usage

plotAnnoBar(
  x,
  xlab = "",
  ylab = "Percentage(%)",
  title = "Feature Distribution",
  ...
)

## S4 method for signature 'list'
plotAnnoBar(
  x,
  xlab = "",
  ylab = "Percentage(%)",
  title = "Feature Distribution",
  ...
)

plotAnnoBar(x, xlab="", ylab='Percentage(%)',title="Feature Distribution", ...)

Arguments

x

csAnno instance

xlab

xlab

ylab

ylab

title

title

...

additional paramter

Value

plot

Author(s)

Guangchuang Yu https://guangchuangyu.github.io


plotAnnoBar.data.frame

Description

plot feature distribution based on their chromosome region

Usage

plotAnnoBar.data.frame(
  anno.df,
  xlab = "",
  ylab = "Percentage(%)",
  title = "Feature Distribution",
  categoryColumn
)

Arguments

anno.df

annotation stats

xlab

xlab

ylab

ylab

title

plot title

categoryColumn

category column

Details

plot chromosome region features

Value

bar plot that summarize genomic features of peaks

Author(s)

Guangchuang Yu https://yulab-smu.top

See Also

annotatePeak plotAnnoPie


plotAnnoPie method generics

Description

plotAnnoPie method for csAnno instance

Usage

plotAnnoPie(
  x,
  ndigit = 2,
  cex = 0.9,
  col = NA,
  legend.position = "rightside",
  pie3D = FALSE,
  radius = 0.8,
  ...
)

plotAnnoPie(x,ndigit=2,cex=0.9,col=NA,legend.position="rightside",pie3D=FALSE,radius=0.8,...)

Arguments

x

csAnno instance

ndigit

number of digit to round

cex

label cex

col

color

legend.position

topright or other.

pie3D

plot in 3D or not

radius

radius of the pie

...

extra parameter

Value

plot

Author(s)

Guangchuang Yu https://guangchuangyu.github.io


plotAnnoPie

Description

pieplot from peak genomic annotation

Usage

plotAnnoPie.csAnno(
  x,
  ndigit = 2,
  cex = 0.8,
  col = NA,
  legend.position = "rightside",
  pie3D = FALSE,
  radius = 0.8,
  ...
)

Arguments

x

csAnno object

ndigit

number of digit to round

cex

label cex

col

color

legend.position

topright or other.

pie3D

plot in 3D or not

radius

radius of Pie

...

extra parameter

Value

pie plot of peak genomic feature annotation

Author(s)

Guangchuang Yu https://yulab-smu.top

See Also

annotatePeak plotAnnoBar

Examples

## Not run: 
require(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
peakfile <- system.file("extdata", "sample_peaks.txt", package="chipseeker")
peakAnno <- annotatePeak(peakfile, TxDb=txdb)
plotAnnoPie(peakAnno)

## End(Not run)

plotAvgProf

Description

plot the profile of peaks

Usage

plotAvgProf(
  tagMatrix,
  xlim,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  conf,
  facet = "none",
  free_y = TRUE,
  origin_label = "TSS",
  verbose = TRUE,
  ...
)

Arguments

tagMatrix

tagMatrix or a list of tagMatrix

xlim

xlim

xlab

x label

ylab

y label

conf

confidence interval

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

origin_label

label of the center

verbose

print message or not

...

additional parameter

Value

ggplot object

Author(s)

G Yu; Y Yan


plotAvgProf.binning

Description

plot the profile of peaks by binning

Usage

plotAvgProf.binning(
  tagMatrix,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  conf,
  facet = "none",
  free_y = TRUE,
  upstream = NULL,
  downstream = NULL,
  label,
  ...
)

Arguments

tagMatrix

tagMatrix or a list of tagMatrix

xlab

x label

ylab

y label

conf

confidence interval

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled

upstream

rel object reflects the percentage of flank extension, e.g rel(0.2) integer reflects the actual length of flank extension or TSS region NULL reflects the gene body with no extension

downstream

rel object reflects the percentage of flank extension, e.g rel(0.2) integer reflects the actual length of flank extension or TSS region NULL reflects the gene body with no extension

label

label

...

additional parameter

Value

ggplot object


plotAvgProf

Description

plot the profile of peaks that align to flank sequences of TSS

Usage

plotAvgProf2(
  peak,
  weightCol = NULL,
  TxDb = NULL,
  upstream = 1000,
  downstream = 1000,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  conf,
  facet = "none",
  free_y = TRUE,
  verbose = TRUE,
  ignore_strand = FALSE,
  ...
)

Arguments

peak

peak file or GRanges object

weightCol

column name of weight

TxDb

TxDb object

upstream

upstream position

downstream

downstream position

xlab

xlab

ylab

ylab

conf

confidence interval

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

verbose

print message or not

ignore_strand

ignore the strand information or not

...

additional parameter

Details

This function is the old function of plotPeakProf2. It can only plot the start site region of gene.

Value

ggplot object

Author(s)

G Yu, Ming L


plotDistToTSS method generics

Description

plotDistToTSS method for csAnno instance

Usage

plotDistToTSS(
  x,
  distanceColumn = "distanceToTSS",
  xlab = "",
  ylab = "Binding sites (%) (5'->3')",
  title = "Distribution of transcription factor-binding loci relative to TSS",
  ...
)

## S4 method for signature 'list'
plotDistToTSS(
  x,
  distanceColumn = "distanceToTSS",
  xlab = "",
  ylab = "Binding sites (%) (5'->3')",
  title = "Distribution of transcription factor-binding loci relative to TSS",
  distanceBreaks = c(0, 1000, 3000, 5000, 10000, 1e+05),
  palette = NULL,
  ...
)

plotDistToTSS(x,distanceColumn="distanceToTSS", xlab="",
ylab="Binding sites (%) (5'->3')",
title="Distribution of transcription factor-binding loci relative to TSS",...)

Arguments

x

csAnno instance

distanceColumn

distance column name

xlab

xlab

ylab

ylab

title

title

...

additional parameter

distanceBreaks

breaks of distance, default is 'c(0, 1000, 3000, 5000, 10000, 100000)'

palette

palette name for coloring different distances. Run 'RColorBrewer::display.brewer.all()' to see all applicable values.

Value

plot

Author(s)

Guangchuang Yu https://guangchuangyu.github.io


plotDistToTSS.data.frame

Description

plot feature distribution based on the distances to the TSS

Usage

plotDistToTSS.data.frame(
  peakDist,
  distanceColumn = "distanceToTSS",
  distanceBreaks = c(0, 1000, 3000, 5000, 10000, 1e+05),
  palette = NULL,
  xlab = "",
  ylab = "Binding sites (%) (5'->3')",
  title = "Distribution of transcription factor-binding loci relative to TSS",
  categoryColumn = ".id"
)

Arguments

peakDist

peak annotation

distanceColumn

column name of the distance from peak to nearest gene

distanceBreaks

default is 'c(0, 1000, 3000, 5000, 10000, 100000)'

palette

palette name for coloring different distances. Run 'RColorBrewer::display.brewer.all()' to see all applicable values.

xlab

x label

ylab

y lable

title

figure title

categoryColumn

category column, default is ".id"

Value

bar plot that summarize distance from peak to TSS of the nearest gene.

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

See Also

annotatePeak

Examples

## Not run: 
require(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
peakfile <- system.file("extdata", "sample_peaks.txt", package="ChIPseeker")
peakAnno <- annotatePeak(peakfile, TxDb=txdb)
plotDistToTSS(peakAnno)

## End(Not run)

internal function for plotPeakProf_MultiWindows

Description

internal function for plotPeakProf_MultiWindows

Usage

plotMultiProf(
  tagMatrix,
  conf,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  facet = "none",
  free_y = TRUE,
  ...
)

Arguments

tagMatrix

tagMatrix

conf

confidence interval

xlab

xlab

ylab

ylab

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

...

additional parameter


internal function

Description

internal function

Usage

plotMultiProf.binning(
  tagMatrix,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  conf,
  facet = "none",
  free_y = TRUE,
  upstream = NULL,
  downstream = NULL,
  label,
  ...
)

Arguments

tagMatrix

tagMatrix

xlab

xlab

ylab

ylab

conf

confidence interval

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

upstream

the upstream extension

downstream

the downstream extension

label

the label of the center

...

additional parameter


internal function

Description

internal function

Usage

plotMultiProf.binning.internal(
  tagMatrix,
  conf,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  facet = "none",
  free_y = TRUE,
  upstream = NULL,
  downstream = NULL,
  label,
  ...
)

Arguments

tagMatrix

tagMatrix

conf

confidence interval

xlab

xlab

ylab

ylab

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

upstream

the upstream extension

downstream

the downstream extension

label

the label of the center

...

additional parameter


internal function

Description

internal function

Usage

plotMultiProf.normal(
  tagMatrix,
  xlim,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  conf,
  facet = "none",
  free_y = TRUE,
  origin_label = "TSS",
  verbose = TRUE,
  ...
)

Arguments

tagMatrix

tagMatrix

xlim

xlim

xlab

xlab

ylab

ylab

conf

confidence interval

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

origin_label

the label of the center

verbose

print message or not

...

additional parameter


internal function

Description

internal function

Usage

plotMultiProf.normal.internal(
  tagMatrix,
  conf,
  xlim = c(-3000, 3000),
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  facet = "row",
  free_y = TRUE,
  origin_label,
  ...
)

Arguments

tagMatrix

tagMatrix

conf

confidence interval

xlim

xlim

xlab

xlab

ylab

ylab

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

origin_label

the label of the center

...

additional parameter


plotPeakProf_MultiWindows

Description

plot the profile of peaks ' plotPeakProf_MultiWindows() is almost the same as plotPeakProf2(), having the main difference of accepting two or more granges objects. Accepting more granges objects can help compare the same peaks in different windows.

Usage

plotPeakProf(
  tagMatrix = NULL,
  peak,
  upstream,
  downstream,
  conf,
  by,
  type,
  windows_name = NULL,
  weightCol = NULL,
  TxDb = NULL,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  facet = "row",
  free_y = TRUE,
  verbose = TRUE,
  nbin = NULL,
  ignore_strand = FALSE,
  ...
)

Arguments

tagMatrix

tagMatrix or a list of tagMatrix

peak

peak file or GRanges object

upstream

upstream position

downstream

downstream position

conf

confidence interval

by

feature of interest

type

one of "start_site", "end_site", "body"

windows_name

the name for each window, which will also be showed in the picture as labels

weightCol

column name of weight

TxDb

TxDb object or self-made granges objects

xlab

xlab

ylab

ylab

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

verbose

print message or not

nbin

the amount of bines

ignore_strand

ignore the strand information or not

...

additional parameter

Details

TxDb parameter can accept txdb object. But many regions can not be obtained by txdb object. In this case, Users can provide self-made granges served the same role as txdb object and pass to TxDb object.

by the features of interest.

(1) if users use txdb, by can be one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'. These features can be obtained by functions from txdb object.

(2) if users use self-made granges object, by can be everything. Because this by will not pass to functions to get features, which is different from the case of using txdb object. This by is only used to made labels showed in picture.

type means the property of the region. one of the "start site", "end site" and "body".

upstream and downstream parameter have different usages:

(1) if type == 'body', upstream and downstream can use to extend the flank of body region.

(2) if type == 'start_site'/'end_site', upstream and downstream refer to the upstream and downstream of the start_site or the end_site.

weightCol refers to column in peak file. This column acts as a weight value. Details see https://github.com/YuLab-SMU/ChIPseeker/issues/15

nbin refers to the number of bins. getTagMatrix() provide a binning method to get the tag matrix.

There are two ways input a list of window.

(1) Users can input a list of self-made granges objects

(2) Users can input a list of by and only one type. In this way, plotPeakProf_MultiWindows() can made a list of window from txdb object based on by and type.

Warning:

(1) All of these window should be the same type. It means users can only compare a list of "start site"/"end site"/"body region" with the same upstream and downstream.

(2) So it will be only one type and several by.

(3) Users can make window by txdb object or self-made granges object. Users can only choose one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR' or 'UTR' in the way of using txdb object. User can input any by in the way of using self-made granges object.

(4) Users can mingle the by designed for the two ways. plotPeakProf_MultiWindows can accpet the hybrid by. But the above rules should be followed.

https://github.com/YuLab-SMU/ChIPseeker/issues/189

Value

ggplot object


plotPeakProf_MultiWindows

Description

plot the profile of peaks in two or more windows

Usage

plotPeakProf_MultiWindows(
  peak,
  upstream,
  downstream,
  conf,
  by,
  type,
  windows_name = NULL,
  weightCol = NULL,
  TxDb = NULL,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  facet = "row",
  free_y = TRUE,
  verbose = TRUE,
  nbin = NULL,
  ignore_strand = FALSE,
  ...
)

Arguments

peak

peak file or GRanges object

upstream

upstream position

downstream

downstream position

conf

confidence interval

by

feature of interest

type

one of "start_site", "end_site", "body"

windows_name

the name for each window, which will also be showed in the picture as labels

weightCol

column name of weight

TxDb

TxDb object or self-made granges objects

xlab

xlab

ylab

ylab

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

verbose

print message or not

nbin

the amount of bines

ignore_strand

ignore the strand information or not

...

additional parameter

Details

This function comes from https://github.com/YuLab-SMU/ChIPseeker/issues/189 ' plotPeakProf_MultiWindows() is almost the same as plotPeakProf2(), having the main difference of accepting two or more granges objects. Accepting more granges objects can help compare the same peaks in different windows.

TxDb parameter can accept txdb object. But many regions can not be obtained by txdb object. In this case, Users can provide self-made granges served the same role as txdb object and pass to TxDb object.

by the features of interest.

(1) if users use txdb, by can be one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'. These features can be obtained by functions from txdb object.

(2) if users use self-made granges object, by can be everything. Because this by will not pass to functions to get features, which is different from the case of using txdb object. This by is only used to made labels showed in picture.

type means the property of the region. one of the "start site", "end site" and "body".

upstream and downstream parameter have different usages:

(1) if type == 'body', upstream and downstream can use to extend the flank of body region.

(2) if type == 'start_site'/'end_site', upstream and downstream refer to the upstream and downstream of the start_site or the end_site.

weightCol refers to column in peak file. This column acts as a weight value. Details see https://github.com/YuLab-SMU/ChIPseeker/issues/15

nbin refers to the number of bins. getTagMatrix() provide a binning method to get the tag matrix.

There are two ways input a list of window.

(1) Users can input a list of self-made granges objects

(2) Users can input a list of by and only one type. In this way, plotPeakProf_MultiWindows() can made a list of window from txdb object based on by and type.

Warning:

(1) All of these window should be the same type. It means users can only compare a list of "start site"/"end site"/"body region" with the same upstream and downstream.

(2) So it will be only one type and several by.

(3) Users can make window by txdb object or self-made granges object. Users can only choose one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR' or 'UTR' in the way of using txdb object. User can input any by in the way of using self-made granges object.

(4) Users can mingle the by designed for the two ways. plotPeakProf_MultiWindows can accpet the hybrid by. But the above rules should be followed.

Value

ggplot object


plotPeakProf2

Description

plot the profile of peaks automatically

Usage

plotPeakProf2(
  peak,
  upstream,
  downstream,
  conf,
  by,
  type,
  weightCol = NULL,
  TxDb = NULL,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  facet = "none",
  free_y = TRUE,
  verbose = TRUE,
  nbin = NULL,
  ignore_strand = FALSE,
  ...
)

Arguments

peak

peak file or GRanges object

upstream

upstream position

downstream

downstream position

conf

confidence interval

by

e.g. 'gene', 'transcript', 'exon' or features of interest(e.g. "enhancer")

type

one of "start_site", "end_site", "body"

weightCol

column name of weight

TxDb

TxDb object, or self-made granges object

xlab

xlab

ylab

ylab

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

verbose

print message or not

nbin

the amount of nbines

ignore_strand

ignore the strand information or not

...

additional parameter

Details

peak stands for the peak file.

by the features of interest.

(1) if users use txdb, by can be one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'. These features can be obtained by functions from txdb object.

(2) if users use self-made granges object, by can be everything. Because this by will not pass to functions to get features, which is different from the case of using txdb object. This by is only used to made labels showed in picture.

type means the property of the region. one of the "start site", "end site" and "body".

upstream and downstream parameter have different usages:

(1) if type == 'body', upstream and downstream can use to extend the flank of body region.

(2) if type == 'start_site'/'end_site', upstream and downstream refer to the upstream and downstream of the start_site or the end_site.

weightCol refers to column in peak file. This column acts as a weight vaule. Details see https://github.com/YuLab-SMU/ChIPseeker/issues/15

nbin refers to the number of bins, providing a binning method to get the tag matrix.

TxDb parameter can accept txdb object. But many regions can not be obtained by txdb object. In this case, Users can provide self-made granges served the same role as txdb object and pass to TxDb object.

plotPeakProf2() is different from the plotPeakProf(). plotPeakProf2() do not need to provide window parameter, which means plotPeakProf2() will call relevent functions to make window automatically.

Value

ggplot object

Author(s)

G Yu, Ming Li


readPeakFile

Description

read peak file and store in data.frame or GRanges object

Usage

readPeakFile(peakfile, as = "GRanges", ...)

Arguments

peakfile

peak file

as

output format, one of GRanges or data.frame

...

additional parameter (pass to 'utils::read.delim()')

Value

peak information, in GRanges or data.frame object

Author(s)

G Yu

Examples

peakfile <- system.file("extdata", "sample_peaks.txt", package="ChIPseeker")
peak.gr <- readPeakFile(peakfile, as="GRanges")
peak.gr

seq2gene

Description

annotate genomic regions to genes in many-to-many mapping

Usage

seq2gene(seq, tssRegion, flankDistance, TxDb, sameStrand = FALSE)

Arguments

seq

genomic regions in GRanges object

tssRegion

TSS region

flankDistance

flanking search radius

TxDb

TranscriptDb object

sameStrand

logical whether find nearest/overlap gene in the same strand

Details

This funciton associates genomic regions with coding genes in a many-to-many mapping. It first maps genomic regions to host genes (either located in exon or intron), proximal genes (located in promoter regions) and flanking genes (located in upstream and downstream within user specify distance).

Value

gene vector

Author(s)

Guangchuang Yu

Examples

## Not run: 
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
TxDb <- TxDb.Hsapiens.UCSC.hg19.knownGene
file <- getSampleFiles()[[1]] # a bed file
gr <- readPeakFile(file)
genes <- seq2gene(gr, tssRegion=c(-1000, 1000), flankDistance = 3000, TxDb) 

## End(Not run)

show method

Description

show method for csAnno instance

Usage

show(object)

Arguments

object

A csAnno instance

Value

message

Author(s)

Guangchuang Yu https://guangchuangyu.github.io


shuffle

Description

shuffle the position of peak

Usage

shuffle(peak.gr, TxDb)

Arguments

peak.gr

GRanges object

TxDb

TxDb

Value

GRanges object

Author(s)

G Yu


tagHeatmap

Description

plot the heatmap of tagMatrix

Usage

tagHeatmap(
  tagMatrix,
  xlab = "",
  ylab = "",
  title = NULL,
  palette = "RdBu",
  nrow = NULL,
  ncol = NULL
)

Arguments

tagMatrix

tagMatrix or a list of tagMatrix

xlab

xlab

ylab

ylab

title

title

palette

palette to be filled in,details see scale_colour_brewer

nrow

the nrow of plotting a list of peak

ncol

the ncol of plotting a list of peak

Value

figure

Author(s)

G Yu


upsetplot method

Description

upsetplot method generics

Usage

upsetplot(x, ...)

Arguments

x

A csAnno instance

...

additional parameter

Value

plot

Author(s)

Guangchuang Yu https://guangchuangyu.github.io


vennpie method generics

Description

vennpie method generics

Usage

vennpie(x, r = 0.2, cex = 1.2, ...)

vennpie(x, r = 0.2, cex=1.2, ...)

Arguments

x

A csAnno instance

r

initial radius

cex

value to adjust legend

...

additional parameter

Value

plot

Author(s)

Guangchuang Yu https://guangchuangyu.github.io


vennplot

Description

plot the overlap of a list of object

Usage

vennplot(Sets, by = "gplots", ...)

Arguments

Sets

a list of object, can be vector or GRanges object

by

one of gplots, ggVennDiagram or Vennerable

...

extra parameters using ggVennDiagram. Details see ggVennDiagram

Details

There are two ways to plot, which users can specify through 'by'.

The first way is to use 'gplots' packages, by setting 'by = gplots'. This method is default method. The venn plot produced through this way has no color.

The second way is to use 'ggVennDiagram' packages, by setting 'by = ggVennDiagram'. The venn plot produced through this way has colors which can be defined by users using ggplot2 grammar e.g.(scale_fill_distiller()). And users can specify any details, like digital number, text size and showing percentage or not, by inputting '...' extra parameters.

Value

venn plot that summarize the overlap of peaks from different experiments or gene annotation from different peak files.

Author(s)

G Yu

Examples

## example not run
## require(TxDb.Hsapiens.UCSC.hg19.knownGene)
## txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
## peakfiles <- getSampleFiles()
## peakAnnoList <- lapply(peakfiles, annotatePeak)
## names(peakAnnoList) <- names(peakfiles)
## genes= lapply(peakAnnoList, function(i) as.data.frame(i)$geneId)
## vennplot(genes)

vennplot.peakfile

Description

vennplot for peak files

Usage

vennplot.peakfile(files, labels = NULL)

Arguments

files

peak files

labels

labels for peak files

Value

figure

Author(s)

G Yu