Quantify windows by summing across positions in each of Nmod and Nvalid

Calculate sums of per-position Nmod and Nvalid counts for positions that overlap windows in gr, and calculate FracMod as the ratio between the two.

Usage

sumNmodNvalid(se, gr, includeEmpty = FALSE)

Arguments

se

A RangedSummarizedExperiment object, as generated by readModBam(..., level = "summary") (i.e. with the assays "Nmod" and "Nvalid").

gr

A GRanges object defining the windows to quantify.

includeEmpty

Logical scalar. If TRUE, include also windows without overlapping modified bases in the output (with zero counts in both the Nmod and Nvalid assays).

Value

A RangedSummarizedExperiment object with one row per window defined by gr and the window quantifications contained in the assays "Nmod", "Nvalid" and "FracMod". This object is suitable for differential analysis by getDifferentiallyModifiedWindows.

Author

Charlotte Soneson, Michael Stadler

Examples

library(GenomicRanges)
library(SummarizedExperiment)
modbamfiles <- system.file("extdata",
                           c("6mA_1_10reads.bam", "6mA_2_10reads.bam"),
                           package = "footprintR")
se <- readModBam(bamfiles = modbamfiles, regions = "chr1:6940000-6940500",
                 level = "summary", modbase = "a", trim = TRUE,
                 BPPARAM = BiocParallel::SerialParam())
s <- seq(6940000, 6940400, by = 100)
windowgr <- GRanges(seqnames = "chr1",
                    ranges = IRanges(start = s, width = 100, names = letters[1:5]))
seSum <- sumNmodNvalid(se = se, gr = windowgr)
seSum
#> class: RangedSummarizedExperiment 
#> dim: 5 2 
#> metadata(1): readLevelData
#> assays(3): Nmod Nvalid FracMod
#> rownames(5): a b c d e
#> rowData names(0):
#> colnames(2): s1 s2
#> colData names(2): sample modbase
assay(seSum, "Nvalid")
#>   s1 s2
#> a 99 55
#> b 91 63
#> c 51 52
#> d 82 68
#> e 76 41