protein_inference: Protein Inference

In vladpetyuk/vp.misc: Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

Description

A function for inferring parsimonious peptide to protein mapping.

Usage

protein_inference(x, Accession = "Accession", PepSeq = "PepSeq")

Arguments

x	table (data.frame, data.frame or tbl_df) with one column correspoding to peptides and the other to proteins or in general case accessions
Accession	character corresponding to column name with protein accesssions
PepSeq	character corresponding to column name with peptide sequences

Value

data.frame with two additional columns

UniqueAndRazor

TRUE if raw correspond to unique or razor peptide to protein mapping

JustifiedAccession

TRUE if protein has any unique peptide that justify its presence

Examples

library(tibble)
x <- tribble(
    ~pep, ~prot,
    "AAAAK", "P1",
    "CCCCK", "P1",
    "LLLLK", "P1",
    "AAAAK", "P2",
    "DDDDK", "P2",
    "AAAAK", "P3") 
protein_inference(x, Accession = "prot", PepSeq = "pep")    

vladpetyuk/vp.misc documentation built on June 25, 2021, 6:35 a.m.