featureAlignedExtendSignal: extract signals in given ranges from bam files

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

extract signals in given ranges from bam files

Description

extract signals in the given feature ranges from bam files (DNAseq only). The reads will be extended to estimated fragement length.

Usage

featureAlignedExtendSignal(
  bamfiles,
  index = bamfiles,
  feature.gr,
  upstream,
  downstream,
  n.tile = 100,
  fragmentLength,
  librarySize,
  pe = c("auto", "PE", "SE"),
  adjustFragmentLength,
  gal,
  ...
)

Arguments

bamfiles	The file names of the 'BAM' ('SAM' for asBam) files to be processed.
index	The names of the index file of the 'BAM' file being processed; this is given without the '.bai' extension.
feature.gr	An object of GRanges with identical width.
upstream, downstream	upstream or dwonstream from the feature.gr.
n.tile	The number of tiles to generate for each element of feature.gr, default is 100
fragmentLength	Estimated fragment length.
librarySize	Estimated library size.
pe	Pair-end or not. Default auto.
adjustFragmentLength	A numberic vector with length 1. Adjust the fragments/reads length to.
gal	A GAlignmentsList object or a list of GAlignmentPairs. If bamfiles is missing, gal is required.
...	Not used.

Value

A list of matrix. In each matrix, each row record the signals for corresponding feature.

Author(s)

Jianhong Ou

See Also

See Also as featureAlignedSignal, estLibSize, estFragmentLength

Examples

 if(interactive() || Sys.getenv("USER")=="jianhongou"){
    path <- system.file("extdata", package="MMDiffBamSubset")
    if(file.exists(path)){
        WT.AB2 <- file.path(path, "reads", "WT_2.bam")
        Null.AB2 <- file.path(path, "reads", "Null_2.bam")
        Resc.AB2 <- file.path(path, "reads", "Resc_2.bam")
        peaks <- file.path(path, "peaks", "WT_2_Macs_peaks.xls")
        estLibSize(c(WT.AB2, Null.AB2, Resc.AB2))
        feature.gr <- toGRanges(peaks, format="MACS")
        feature.gr <- feature.gr[seqnames(feature.gr)=="chr1" & 
                             start(feature.gr)>3000000 & 
                             end(feature.gr)<75000000]
        sig <- featureAlignedExtendSignal(c(WT.AB2, Null.AB2, Resc.AB2), 
                               feature.gr=reCenterPeaks(feature.gr, width=1), 
                               upstream = 505,
                               downstream = 505,
                               n.tile=101, 
                               fragmentLength=250,
                               librarySize=1e9)
        featureAlignedHeatmap(sig, reCenterPeaks(feature.gr, width=1010), 
                          zeroAt=.5, n.tile=101)
    }
 }

jianhong/ChIPpeakAnno documentation built on Feb. 2, 2024, 3:26 p.m.