compNucFreq {decompTumor2Sig} | R Documentation

## 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: <rmpiro@gmail.com> or <rosariomichael.piro@polimi.it>

### References

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

[Package decompTumor2Sig version 2.8.0 Index]