surrounding_peptides: The Surrounding Peptide Function

In lukatrkla/lanpAnalysis: lanpAnalysis Analyzes HLA-I-binding Neoantigens Significant for Lung Adenocarcinoma Immunotherapy

Description

Often, the immediate peptides to a mutation are relevant for analyzing a neoantigen. surrounding_peptides finds all neoantigens within seq for geneName that are in the lung cancer database, and returns a dataframe containing the strings for each of these found neoantigens with sides number of flanking peptides in the peptide sequence (in lower case), and the peptides' position.

Usage

surrounding_peptides(geneName, seq, sides = 3)

Arguments

geneName	The string name of the gene.
seq	The string peptide sequence associated with the gene.
sides	The number of peptides you wish to view flanking the ends of seq. By default this is 3.

Value

string

Examples

surrounding_peptides("MAGI2", "GGMNLRIAK...", sides=4)
"(10)rimkNETPVAVLTImiga(26)"

lukatrkla/lanpAnalysis documentation built on Jan. 1, 2021, 8:26 a.m.