kmer_freq: Kmer frequency

Description Usage Arguments

View source: R/kmer_freq.R

Description

Calculate kmer frequency in mutated and non-mutated sites. Apply fisher test

Usage

1
kmer_freq(dataset, ks = 5, pval_cutoff = 0.001, n_keep = 80)

Arguments

dataset

Granges object, with a 'sequence.pyr' column containing sequence region and 'mut.pyr' column containing mutations

ks

Int. Size of kmers to look for

pval_cutoff.

Real. Filtering threshold for fisher test

n_keep.

Int. Number of kmers to keep


lindberg-m/contextendR documentation built on Jan. 8, 2022, 3:16 a.m.