pSNVs: Find phosphorylation related variants (pSNVs)

In omarwagih/rmimp: Predicting the impact of mutations on kinase-substrate phosphorylation

Description

Given mutation data and psites, find variants that exist in the flanking regions of the psite

Usage

pSNVs(md, pd, seqdata, flank = 7)

Arguments

flank	Number of amino acids flanking the psite to be considered
muts	Mutation data as data frame of two columns (1) name of gene or protein (2) mutation in the format X123Y, where X is the reference amino acid and Y is the alternative amino acid.
psites	Phosphorylation data as a data frame of two columns (1) name of gene or protein (2) Position of the phosphorylated residue
seqs	Sequence data as a name list. Names of the list correspond to the gene or protein name. Each entry contains the collapsed sequence.

Examples

# No examples

omarwagih/rmimp documentation built on May 18, 2020, 3:11 p.m.