consensusMatrix_character: Computes a consensus matrix.

In philliplab/yasss: Yet Another Short Sequence Simulator

Description

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

Usage

consensusMatrix_character(x)

Arguments

x	The sequence data as a set of character vectors

Details

Designed to function like consensusMatrix from Biostrings.

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.

philliplab/yasss documentation built on Sept. 7, 2020, 3:28 p.m.