Calculate GC content over genomic ranges — calcGCContentRef • GenomicDistributions

Given a reference genome as a BSgenome object and some ranges on that reference, this function will return a vector of the same length as the granges object, with percent of Cs and Gs.

calcGCContentRef(query, refAssembly)

Arguments

query: A GenomicRanges or GenomicRangesList object with query regions
refAssembly: A character vector specifying the reference genome assembly (*e.g.* 'hg19'). This will be used to grab chromosome sizes with getTSSs.

Value

A numeric vector or list of vectors with the GC percentage of the query regions.

Examples

if (FALSE) { # \dontrun{
refAssembly = 'hg19'
GCcontent = calcGCContentRef(vistaEnhancers, refAssembly)
} # }