coverage-functions: Private functions behind 'cumulativeCTSSdistribution'

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

.getCumsum calculates cumulative sums of tpm along the clusters.

Usage

.getCAGEsignalCoverage(ctss.chr, clusters)

.getCumsumChr2(clusters, ctss, chrom, str)

.getCumsum(ctss, clusters, useMulticore = FALSE, nrCores = NULL)

Arguments

ctss.chr	A 'CTSS.chr“ object (guaranteed to have only one chromosome).
clusters	GRanges as per tagClustersGR().
ctss	GRanges as per CTSScoordinatesGR, with the score of one sample.
chrom	a chromosome name
str	a strand name
useMulticore, nrCores	See clusterCTSS.

Details

'.getCAGEsignalCoverage“ does... Note that strand is not taken into account.

.getCumsumChr2

Value

.getCumsum returns a list of Rle vectors (IRanges package) containing cumulative sum for each cluster (length of list is equal to number of clusters and names of the list components corespond to the name of the corresponding cluster) v.

Examples

library(GenomicRanges)
library(IRanges)
ctss <- CTSS( seqnames = "chr1"
            , IRanges(c(1,3,4,12,14,25,28,31,35), w=1)
            , strand = "+")
score(ctss) <- 1
ctss.chr <- as(ctss, "CTSS.chr")
clusters <- GRanges( seqnames = Rle("chr1")
                   , ranges = IRanges(c(1,12,25,31,32), c(4,14,28,31,33))
                   , strand = "+")
chrom <- "chr1"
str <- "+"
CAGEr:::.getCAGEsignalCoverage(ctss.chr, clusters)
CAGEr:::.getCumsumChr2(clusters, ctss, chrom, str)
ctss      <- CTSSnormalizedTpmGR(exampleCAGEset, "sample1")
ctss      <- ctss[ctss$filteredCTSSidx]
clusters  <- tagClustersGR(exampleCAGEset, "sample1")
clusters.cumsum <- RleList(CAGEr:::.getCumsum(ctss, clusters))
identical( lapply(exampleCAGEset@CTSScumulativesTagClusters[[1]],decode)
         , lapply(clusters.cumsum, decode))
# Not identical if not decoded because Rle method is attached to S4Vectors in one case
# and to IRanges in the other case.
decode(clusters.cumsum[[1]])
ctss[queryHits(findOverlaps(ctss, clusters[1]))]
clusters[1]

ctss      <- CTSSnormalizedTpmGR(exampleCAGEexp, "Zf.30p.dome")
ctss      <- ctss[ctss$filteredCTSSidx]
clusters  <- tagClustersGR(exampleCAGEexp, "Zf.30p.dome")
clusters.cumsum <- CAGEr:::.getCumsum(ctss, head(clusters))
decode(clusters.cumsum[[3]])
ctss[queryHits(findOverlaps(ctss, clusters[3]))]
clusters[3]

CAGEr documentation built on Jan. 17, 2021, 2 a.m.