oncodriveclustl: oncodriveclustl

In msubirana/ergWgsTools: What the Package Does (One Line, Title Case)

Description

Parser for oncodriveclustl

Usage

oncodriveclustl(
  input,
  regions,
  output_dir,
  genome = "hg38",
  cores = 2,
  kmer = 5,
  sigcalc = "region_normalized",
  sw = 11,
  simw = 31,
  cw = 11
)

Arguments

input	File containing mutations
regions	GZIP compressed file with the genomic regions to analyze
output_dir	Output directory to be created
genome	Genome to use. Default hg38.
cores	Cores to use in the analysis.
kmer	K-mer nucleotide context. Default 5.
sigcalc	Signature calculation: mutation frequencies (frequencies) or k-mer mutation counts normalized by k-mer region counts (region_normalized). Default region_normalized
sw	Smoothing window. Default is 11
simw	Simulation window. Default is 31
cw	Cluster window. Default is 11

Examples

## Not run: 
oncodriveclustl(input = 'all_ins.tvs', regions = 'regions.regions', output_dir = 'rst/', genome = 'hg38', cores = 2)

## End(Not run)

msubirana/ergWgsTools documentation built on June 8, 2020, 8:07 a.m.