expressed_regions {recount} | R Documentation |
This function uses the pre-computed mean coverage for a given SRA project to identify the expressed regions (ERs) for a given chromosome. It returns a GRanges-class object with the expressed regions as defined by findRegions.
expressed_regions(project, chr, cutoff, outdir = NULL, maxClusterGap = 300L, chrlen = NULL, verbose = TRUE, ...)
project |
A character vector with one SRA study id. |
chr |
A character vector with the name of the chromosome. |
cutoff |
The base-pair level cutoff to use. |
outdir |
The destination directory for the downloaded file(s) that were
previously downloaded with download_study. If the files are missing,
but |
maxClusterGap |
This determines the maximum gap between candidate ERs. |
chrlen |
The chromosome length in base pairs. If it's |
verbose |
If |
... |
Additional arguments passed to download_study when
|
A GRanges-class object as created by findRegions.
Leonardo Collado-Torres
download_study, findRegions, railMatrix
## Define expressed regions for study SRP009615, chrY if(.Platform$OS.type != 'windows') { ## Reading BigWig files is not supported by rtracklayer on Windows regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L, maxClusterGap = 3000L) } ## Not run: ## Define the regions for multiple chrs regs <- sapply(chrs, expressed_regions, project = 'SRP009615', cutoff = 5L) ## You can then combine them into a single GRanges object if you want to library('GenomicRanges') single <- unlist(GRangesList(regs)) ## End(Not run)