Genomic positions of a motif (CG) — getCGPositions • mesa

Return the genomic positions of the "CG" dinucleotide for the specified BSgenome and chromosomes, located directly with Biostrings.

getCGPositions(BSgenome, chr.select)

Arguments

BSgenome: Character(1). BSgenome package name.
chr.select: Character vector of chromosome names to include (e.g., paste0("chr", 1:22)). If NULL, the standard chromosomes of the BSgenome are used – not every seqlevel. Scaffolds, patches and alt haplotypes are excluded, because scanning all 298 hg19 seqlevels costs ~22 s and ~1.3 GB for positions no read maps to.

Value

A GRanges-class of motif positions.

See also

calculateCGEnrichment, calculateCGEnrichmentGRanges, Biostrings

Examples

# Requires a BSgenome package
# if (requireNamespace("BSgenome.Hsapiens.NCBI.GRCh38", quietly = TRUE)) {
#   getCGPositions("BSgenome.Hsapiens.NCBI.GRCh38", chr.select = "22")
# }