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 1.6.4 Index]