metagenePlot: peak distance to features

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

peak distance to features

Description

Bar plot for distance to features

Usage

metagenePlot(
  peaks,
  AnnotationData,
  PeakLocForDistance = c("middle", "start", "end"),
  FeatureLocForDistance = c("TSS", "middle", "geneEnd"),
  upstream = 1e+05,
  downstream = 1e+05
)

Arguments

peaks	peak list, GRanges object or a GRangesList.
AnnotationData	A GRanges object or a TxDb object.
PeakLocForDistance	Specify the location of peak for calculating distance,i.e., middle means using middle of the peak to calculate distance to feature, start means using start of the peak to calculate the distance to feature. To be compatible with previous version, by default using start
FeatureLocForDistance	Specify the location of feature for calculating distance,i.e., middle means using middle of the feature to calculate distance of peak to feature, TSS means using start of feature when feature is on plus strand and using end of feature when feature is on minus strand, geneEnd means using end of feature when feature is on plus strand and using start of feature when feature is on minus strand.
upstream, downstream	numeric(1). Upstream or downstream region of features to plot.

Details

the bar heatmap is indicates the peaks around features.

Examples

path <- system.file("extdata", package="ChIPpeakAnno")
files <- dir(path, "broadPeak")
peaks <- sapply(file.path(path, files), toGRanges, format="broadPeak")
peaks <- GRangesList(peaks)
names(peaks) <- sub(".broadPeak", "", basename(names(peaks)))
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
metagenePlot(peaks, TxDb.Hsapiens.UCSC.hg19.knownGene)

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.