binnedCoverage {DEScan2} | R Documentation |
this function computes the coverage over a binned chromosome, starting from a per base computed coverage.
binnedCoverage(bins, numvar, mcolname, covMethod = c("max", "mean", "sum", "min"), roundingMethod = c("none", "floor", "ceiling", "round"))
bins |
a GRanges object representing a chromosome binned. |
numvar |
an RleList representing the per base coverage over the chr. |
mcolname |
the name of column where the sum have to be stored. |
covMethod |
a method to apply for the computing of the coverate it can be one of "max", "mean", "sum", "min". ("max" is default) |
roundingMethod |
a method to apply to round the computations it can be one of "none", "floor", "ceiling", "round". It's useful only when using covMethod="mean". ("none" is default) |
the bins GRanges with the mcolname attached
## dividing one chromosome in bins of 50 bp each seqinfo <- GenomeInfoDb::Seqinfo(genome="mm9") bins <- GenomicRanges::tileGenome( seqlengths=GenomeInfoDb::seqlengths(seqinfo)[1], tilewidth=50, cut.last.tile.in.chrom=TRUE) gr <- GenomicRanges::GRanges(seqnames = S4Vectors::Rle("chr1", 100), ranges=IRanges::IRanges(start = seq(from=10, to=1000, by=10), end=seq(from=20, to=1010, by = 10))) cov <- GenomicRanges::coverage(x=gr) (binnedMaxCovGR <- binnedCoverage(bins, cov, "binned_cov")) (binnedMeanCovGR <- binnedCoverage(bins, cov, "binned_cov", covMethod="mean", roundingMethod="floor")) (binnedSumCovGR <- binnedCoverage(bins, cov, "binned_cov", covMethod="sum"))