Quantify windows by calculating a Fourier-transform-based phasing score

Calculate a phasing score by decomposing FracMod in a window into frequency components and extract the numCoef-th coefficient.

Usage

phasingScoreFourier(se, gr, numCoef = 5)

Arguments

se: A RangedSummarizedExperiment object, as generated by readModBam(..., level = "summary") (i.e. with the assays "Nvalid" and "FracMod").
gr: A GRanges object defining the windows to quantify. Here, the width of the ranges in gr have to be an integer multiple of the period of interest (typically width(gr) = (numCoef - 1) * periodOfInterest).
numCoef: An integer scalar giving the Fourier coefficient to extract. The coefficient corresponds to a period of width(gr) / (numCoef - 1).

Value

A RangedSummarizedExperiment object with one row per window defined by gr and the window phasing scores for periodic signals with a frequency defined by "numCoef". This object is suitable for transformation by getRangesWithAssayValues.

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")
rng <- GRanges("chr1", IRanges(6940000, 6943600))
windowStep <- 180
windowSize <- 4 * windowStep
s <- seq(start(rng), end(rng) - windowSize + 1, by = windowStep)
windowgr <- GRanges(seqnames = seqnames(rng),
                    ranges = IRanges(start = s, width = windowSize))
se <- readModBam(bamfiles = modbamfiles, regions = rng, level = "summary",
                 modbase = "a", trim = TRUE,
                 BPPARAM = BiocParallel::SerialParam())
seFourier <- phasingScoreFourier(se = se, gr = windowgr, numCoef = 5)
assay(seFourier, "phasingScoreAbs") # amplitude of requested coefficient
#>              s1         s2
#>  [1,] 22.104124 11.7576205
#>  [2,] 27.132726  3.8888579
#>  [3,] 17.332390  0.4179011
#>  [4,]  9.322762  0.0000000
#>  [5,]  8.247887  0.0000000
#>  [6,]  4.598294  0.0000000
#>  [7,]  0.984381  0.0000000
#>  [8,]  0.000000  0.0000000
#>  [9,]  0.000000  0.0000000
#> [10,]  0.000000  0.0000000
#> [11,]  0.000000  0.0000000
#> [12,]  0.000000  0.0000000
#> [13,]  0.000000  0.0000000
#> [14,]  0.000000  0.0000000
#> [15,]  0.000000  0.0000000
#> [16,]  0.000000  0.0000000
#> [17,]  0.000000  0.0000000
assay(seFourier, "phasingScoreRel") # relative amplitude
#>                s1          s2
#>  [1,] 0.032935952 0.008596142
#>  [2,] 0.027635236 0.005619616
#>  [3,] 0.015046715 0.007232441
#>  [4,] 0.009746856         NaN
#>  [5,] 0.010512054         NaN
#>  [6,] 0.008950576         NaN
#>  [7,] 0.006229053         NaN
#>  [8,]         NaN         NaN
#>  [9,]         NaN         NaN
#> [10,]         NaN         NaN
#> [11,]         NaN         NaN
#> [12,]         NaN         NaN
#> [13,]         NaN         NaN
#> [14,]         NaN         NaN
#> [15,]         NaN         NaN
#> [16,]         NaN         NaN
#> [17,]         NaN         NaN