plotCorrelation {ATACseqQC}R Documentation

plot Correlations of multiple samples

Description

plot PCA or heatmap for multiple bamfiles. The correlation is calculated by the counts in promoter regions.

Usage

plotCorrelation(objs, txs, seqlev = intersect(seqlevels(objs[[1]]),
  seqlevels(txs)), upstream = 2000, downstream = 500,
  type = c("heatmap", "PCA"), ...)

Arguments

objs

an object of GAlignmentsList

txs

GRanges of transcripts

seqlev

A vector of characters indicates the sequence levels.

upstream

numeric(1) or integer(1). Start position of promoter. Default is 2000

downstream

numeric(1) or integer(1). End position of promoter. Default is 500

type

Figure type, heatmap or PCA plot.

...

parameters could be passed to downstream functions such as plot for pca or heatmap for heatmap.

Value

A invisible object of GRanges with counts

Author(s)

Jianhong Ou

Examples

library(GenomicRanges)
library(GenomicAlignments)
path <- system.file("extdata", package="ATACseqQC", mustWork=TRUE)
bamfiles <- dir(path, "*.bam$", full.name=TRUE)
gals <- lapply(bamfiles, function(bamfile){
               readBamFile(bamFile=bamfile, tag=character(0), 
                           which=GRanges("chr1", IRanges(1, 1e6)), 
                           asMates=FALSE)
        })
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txs <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
plotCorrelation(GAlignmentsList(gals), txs, seqlev="chr1")

[Package ATACseqQC version 1.8.5 Index]