kmer2StringSet: Convert a vector of k-mers into a DNAStringSet

In steveped/fastqcWrap: Provides wrappers to FastQC from within R

Description

Convert a vector of k-mers into a DNAStringSet

Usage

kmer2StringSet(seq, pos, ..., pad = "N")

Arguments

seq	a vector of k-mers
pos	a vector of positions within a set of reads
...	not used
pad	the DNA base to be added when shifting k-mers

Details

Take a vector of k-mers and their repective positions within a set of reads, then shift accordingly. The DNA_ALPHBET value N is added by default to enable easy integration with other functions in the package Biostrings.

To find a possible consensus sequence, simply pass the output to Biobase::consensusString()

Value

a DNAStringSet

Author(s)

Steve Pederson <[e-mail]>

steveped/fastqcWrap documentation built on May 30, 2019, 5:39 p.m.