compNucFreq: Compute nucleotide frequencies (internal function)

In rmpiro/decompTumor2Sig: Decomposition of individual tumors into mutational signatures by signature refitting

Compute nucleotide frequencies (internal function)

Description

Compute nucleotide frequencies for a reference genome and a region set.

Usage

compNucFreq(refGenome, regions=NULL, numBases=1, mergeByRevComp=TRUE)

Arguments

refGenome	Reference genome (BSgenome)
regions	(Optional) Regions (GRanges); default: NULL (whole genome).
numBases	(Optional) Sequence pattern length for which to compute frequencies (e.g., '3' for trinucleotides). Default: 1 (single nucleotides).
mergeByRevComp	(Optional) Reduce redundancy by merging counts for reverse complement sequence patterns. This function allows this only for sequence patterns with odd length (e.g., single nucleotides, trinucleotides). Default: TRUE.

Value

Vector of computed nucleotide frequencies

Author(s)

Rosario M. Piro
Politecnico di Milano
Maintainer: Rosario M. Piro
E-Mail: <[e-mail]> or <[e-mail]>

References

http://rmpiro.net/decompTumor2Sig/
Krueger, Piro (2019) decompTumor2Sig: Identification of mutational signatures active in individual tumors. BMC Bioinformatics 20(Suppl 4):152.

rmpiro/decompTumor2Sig documentation built on May 15, 2022, 3:27 a.m.