featureAlignedExtendSignal {ChIPpeakAnno} | R Documentation

## 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)
        }
     }

[Package ChIPpeakAnno version 3.24.2 Index]