applyNFsGRanges {BRGenomics} | R Documentation |
Convenience function for multiplying signal counts in one or more GRanges object by their normalization factors.
applyNFsGRanges( dataset.gr, NF, field = "score", ncores = getOption("mc.cores", 2L) )
dataset.gr |
A GRanges object with signal data in one or more metadata fields, or a list of such GRanges objects. |
NF |
One or more normalization factors to apply by multiplication. The
number of normalization factors should match the number of datasets in
|
field |
The metadata field(s) in |
ncores |
The number of cores to use for computations. Multicore only used if there are multiple datasets present. |
A GRanges object, or a list of GRanges objects.
Mike DeBerardine
# Apply NFs to a single GRanges gr <- GRanges(seqnames = "chr1", ranges = IRanges(1:3, 3:5), strand = c("+", "+", "-"), score = c(2, 3, 4)) gr applyNFsGRanges(gr, NF = 0.5, ncores = 1) # Apply NFs to a list of GRanges gr2 <- gr ranges(gr2) <- IRanges(4:6, 5:7) grl <- list(gr, gr2) grl applyNFsGRanges(grl, NF = c(0.5, 0.75), ncores = 1) # Apply NFs to a multiplexed GRanges gr_multi <- gr names(mcols(gr_multi)) <- "gr1" gr_multi$gr2 <- c(3, 5, 7) gr_multi applyNFsGRanges(gr_multi, NF = c(2, 3), field = c("gr1", "gr2"), ncores = 1)