fasta2num: fasta2num

In markheron/pRon: pretty Representations of oligo-nucleotides

Description

Transforms a DNAStringSet with equal length objects into a matrix of numeric representation of the oligo-nucleotides. Any oligo-nucleotide with a letter differing from A,C,G,T is represented as **NA**

Usage

fasta2num(fastas, oligo_length, method = "lookupTable",
  simplify = TRUE)

Arguments

fastas	(DNAStringSet) of same length fasta sequences that should be converted (single DNAString also possible)
oligo_length	(numeric) length of the oligo-nucleotides to use.
method	("lookupTable") one of"as.integer", "lookupTable", "slidingView" and "memoryLimited" they are different implementations that have different speed/memory tradeoffs
simplify	(bool) in the case of a single fasta sequence, should a vector be returned instead of a matrix

Value

matrix (or vector) of numeric representation of the fastas

markheron/pRon documentation built on Feb. 18, 2020, 12:33 a.m.