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)
)A GRanges object with signal data in one or more metadata fields, or a list of such GRanges objects.
One or more normalization factors to apply by multiplication. The
number of normalization factors should match the number of datasets in
dataset.gr.
The metadata field(s) in dataset.gr that contain signal
to be normalized.
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.
# Apply NFs to a single GRanges
gr <- GRanges(seqnames = "chr1",
ranges = IRanges(1:3, 3:5),
strand = c("+", "+", "-"),
score = c(2, 3, 4))
gr
#> GRanges object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 1-3 + | 2
#> [2] chr1 2-4 + | 3
#> [3] chr1 3-5 - | 4
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
applyNFsGRanges(gr, NF = 0.5, ncores = 1)
#> GRanges object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 1-3 + | 1.0
#> [2] chr1 2-4 + | 1.5
#> [3] chr1 3-5 - | 2.0
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# Apply NFs to a list of GRanges
gr2 <- gr
ranges(gr2) <- IRanges(4:6, 5:7)
grl <- list(gr, gr2)
grl
#> [[1]]
#> GRanges object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 1-3 + | 2
#> [2] chr1 2-4 + | 3
#> [3] chr1 3-5 - | 4
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> [[2]]
#> GRanges object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 4-5 + | 2
#> [2] chr1 5-6 + | 3
#> [3] chr1 6-7 - | 4
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
applyNFsGRanges(grl, NF = c(0.5, 0.75), ncores = 1)
#> [[1]]
#> GRanges object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 1-3 + | 1.0
#> [2] chr1 2-4 + | 1.5
#> [3] chr1 3-5 - | 2.0
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> [[2]]
#> GRanges object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 4-5 + | 1.50
#> [2] chr1 5-6 + | 2.25
#> [3] chr1 6-7 - | 3.00
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
# Apply NFs to a multiplexed GRanges
gr_multi <- gr
names(mcols(gr_multi)) <- "gr1"
gr_multi$gr2 <- c(3, 5, 7)
gr_multi
#> GRanges object with 3 ranges and 2 metadata columns:
#> seqnames ranges strand | gr1 gr2
#> <Rle> <IRanges> <Rle> | <numeric> <numeric>
#> [1] chr1 1-3 + | 2 3
#> [2] chr1 2-4 + | 3 5
#> [3] chr1 3-5 - | 4 7
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
applyNFsGRanges(gr_multi, NF = c(2, 3), field = c("gr1", "gr2"),
ncores = 1)
#> GRanges object with 3 ranges and 2 metadata columns:
#> seqnames ranges strand | gr1 gr2
#> <Rle> <IRanges> <Rle> | <numeric> <numeric>
#> [1] chr1 1-3 + | 4 9
#> [2] chr1 2-4 + | 6 15
#> [3] chr1 3-5 - | 8 21
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths