findMotifChanges: findMotifChanges

In BIMSBbioinfo/slimR: Short Linear Motif (SLiM) Analysis in the context of human diseases

Description

Find out which SLiMs are gained or lost (no longer matching the regex pattern) via point amino acid substitutions in protein sequences

Usage

findMotifChanges(sequence, variants, motifRegex = slimR::motifRegex)

Arguments

sequence	A character string of amino acid sequence
variants	A data.frame consisting of minimum four columns: 1.uniprotAccession, 2.wtAA, 3.mutAA, 4.pos where pos is the mutation position in the sequence, wtAA is the wild-type amino acid (one letter code) in the sequence and mutAA is the mutant amino acid (one letter code).
motifRegex	List of slim regular expressions. By default, the built-in slimR::motifRegex from the ELM database is used.

Value

data.table data.frame object

Examples

glutFastaFile <- system.file("extdata", "glut.fasta", package = 'slimR')
glutFasta <- Biostrings::readAAStringSet(glutFastaFile)

variants <- data.frame('uniprotAccession' = 'P11166', 'pos' = 485, 'wtAA' = 'P', 'mutAA' = 'L')

findMotifChanges(paste(glutFasta), variants, slimR::motifRegex)

BIMSBbioinfo/slimR documentation built on Nov. 4, 2021, 6:48 a.m.