consensusMatrix_seqinr: Computes a consensus matrix.

In philliplab/hypermutR: Detects hypermutation in DNA

Description

Tallies characters at each position for a set of character vectors without any Bioconductor packages.

Usage

consensusMatrix_seqinr(x, ...)

Arguments

x	The sequence data of type SeqFastadna

Details

Designed to function like consensusMatrix from Biostrings.

Note that seqinr uses lower case letters and Biostrings uses upper case letters.

This function can handle upper and lower case input, but will only produce upper case output.

To prevent a dependency on a bioconductor package, this is not properly set up as a method for the consensusMatrix generic defined in Biostrings.

Value

A matrix with columns representing positions in the sequence and rows the allowed characters in IUPAC notation of nucleotides and cells the counts of the respective character at the respective position.

Examples

consensusMatrix_seqinr(ld_seqs)

philliplab/hypermutR documentation built on Sept. 2, 2020, 2:51 p.m.