proteinGroup: Protein inference

In proteoQC: An R package for proteomics data quality control

Description

Protein inference

Usage

proteinGroup(file = NULL, db = "", pepColName = "peptide",
  proColName = "protein", spectrumColName = "index", proSep = ";",
  outfile = NULL, xmx = 1)

Arguments

file	A file containing the information of peptides to proteins.
db	A protein database of fasta format.
pepColName	The column name of peptide sequence.
proColName	The column name of protein ID.
spectrumColName	The column name of spectrum index.
proSep	The separator of protein ID, default is "".
outfile	The output file name of protein group result.
xmx	JAVA -Xm

Author(s)

Bo Wen [e-mail]

Examples

pep.zip <- system.file("extdata/pep.zip", package = "proteoQC")
unzip(pep.zip)
proteinGroup(file = "pep.txt", outfile = "pg.txt")

proteoQC documentation built on Oct. 31, 2019, 3:20 a.m.