applyNFsGRanges: Apply normalization factors to GRanges object
In BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data

Description Usage Arguments Value Author(s) See Also Examples

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 `dataset.gr`.
`field`	The metadata field(s) in `dataset.gr` that contain signal to be normalized.
`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

getSpikeInNFs

# 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)