Utility_Sequence: Utility functions for sequence analysis.

Utility_SequenceR Documentation

Utility functions for sequence analysis.

Description

sequenceFilter filters amino acid sequences so that those containing non-standard letters are excluded.
sequenceSlidingWindow splits the input sequences in a sliding window basis with a fixed window size.
InSilicoMutagenesis generates single-aa-substituted sequences. Currently insertions and deletions are not supported.

Usage

sequenceFilter(peptideSet, peptideLengthSet = 8:11)

sequenceSlidingWindow(peptideSet, windowSize = 3)

InSilicoMutagenesis(
  peptideSet,
  peptideLengthSet = 8:11,
  coreN = parallel::detectCores(logical = F)
)

Arguments

peptideSet

A set of amino acid sequences.

peptideLengthSet

A set of allowed amino acid sequence lengths. Peptides not falling in this range will be discarded.

windowSize

A size of the sliding window.

coreN

The number of cores to be used for parallelization.


masato-ogishi/Repitope documentation built on Feb. 14, 2023, 5:47 a.m.