validateVariants: validateVariants

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

Description

This function is used to validate whether the missense variants are consistent with the fasta sequences of the proteins

Usage

validateVariants(df, fasta, nodeN = 1)

Arguments

df	A data.frame or data.table containing minimally the following columns: 1. uniprotAccession 2. wtAA (wild-type amino acid) 3. pos (the position of the wild-type amino acid in the protein sequence)
fasta	AAStringSet object of protein sequences, in which names of the list items should correspond to the uniprotAccession column of the 'df' input
nodeN	Number of cores to use to parallelise the run

Value

A data.frame consisting of the input data.frame and two additional columns for 1. mappedResidue (the actual residue at the variant position) 2. validity (boolean TRUE/FALSE) showing if the mapped residue matches the wild-type residue in the corresponding variant.

Examples

glutFastaFile <- system.file("extdata", "glut.fasta", package = 'slimR')
glutFasta <- Biostrings::readAAStringSet(glutFastaFile)
data("glutMutations")
val <- validateVariants(df = glutMutations[1:10,], fasta = glutFasta, nodeN = 1)

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