kcount: 'kcount' Counting kmer frequency for a given genome or pseudo...

In yangjl/pseudoRef: Substitute Reference Genome with Sample Specific SNP variants

Description

kcount Counting kmer frequency for a given genome or pseudo genome.

Usage

kcount(fa, feature, kmers = 3:7)

Arguments

fa	Path for the reference fasta file. [string or DNAStringSet/DNAString object]
feature	A data.frame object (BED like, but all 1-based coordinates). [data.frame, 4 required columns: chr, start, end, geneid]
kmers	A vector to indicate kmers to count. Note, k<=15. [vector, default=3:7].

Value

A data.frame of kmer as rows x geneid as columns. [data.frame].

Examples

feature <- data.frame(chr=1, start=seq(from=1, to=10000001, by=1000),
                      end=seq(from=1000, to=11000000, by=1000)[1:10001],
                      geneid=paste0("g", 1:10001))
kcount(fa, feature, kmers=3:7)

yangjl/pseudoRef documentation built on March 30, 2020, 7:47 p.m.