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.
addCovToGR(gr, bwFile, window = 1000, binSize = 1, colname = "chip")
| gr |
|
|---|---|
| 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
|
| 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
|
GRanges as input but with an additional
meta column containing the coverage values for each region as
NumericList.
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) }