addCovToGR {sevenC} | R Documentation

## Add coverage to regions in `GRanges` object.

### Description

This function adds a `NumericList` of coverage (or any other signal in the input bigWig file) to each range in a `GRanges` object. The coverage is reported for a fixed-sized window around the region center. For regions with negative strand, the coverage vector is reversed. The coverage signal is added as new metadata column holding a `NumericList` object. Note, this function does not work on windows because reading of bigWig files is currently not supported on windows.

### Usage

    addCovToGR(gr, bwFile, window = 1000, binSize = 1, colname = "chip")

### Arguments

`gr` | `GRanges` object with genomic regions. It should contain a valid seqinfo object with defined seqlengths.
`bwFile` | File path or connection to BigWig or wig file with coverage to parse from.
`window` | Numeric scalar for window size around the center of ranges in `gr`.
`binSize` | Integer scalar as size of bins to which the coverage values are combined.
`colname` | Character as name of the new column that is created in `gr`.

### Value

`GRanges` as input but with an additional meta column containing the coverage values for each region as `NumericList`.

### Examples

    if (.Platform$OS.type != "windows") {

     # use example bigWig file of ChIP-seq signals on human chromosome 22
     exampleBigWig <- system.file("extdata",
     "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC")

     # use example CTCF moitf location on human chromosome 22
     motifGR <- sevenC::motif.hg19.CTCF.chr22

     # add ChIP-seq signals to motif regions
     motifGR <- addCovToGR(motifGR, exampleBigWig)

     # add ChIP-seq signals as column named "Stat1"
     motifGR <- addCovToGR(motifGR, exampleBigWig, colname = "Stat1")

     # add ChIP-seq signals in windows of 500bp around motif centers
     motifGR <- addCovToGR(motifGR, exampleBigWig, window = 500)

     # add ChIP-seq signals in bins of 10 bp
     motifGR <- addCovToGR(motifGR, exampleBigWig, binSize = 10)

    }

[Package sevenC version 1.12.0 Index]