runTandem: Run X!Tandem

In proteoQC: An R package for proteomics data quality control

Description

Run X!Tandem

run X!Tandem

Usage

runTandem(spectra = "", fasta = "", outdir = "./", outprefix = "",
  cpu = 1, enzyme = 1, xmx = 2, varmod = NULL, fixmod = NULL,
  refine = TRUE, ntt = 1, tol = 10, tolu = "ppm", itol = 0.6,
  itolu = "Daltons", miss = 1)

Arguments

spectra	MS/MS peak list file
fasta	database file
outdir	output directory
outprefix	output file prefix
cpu	The number of CPU used for X!Tandem
enzyme	The ID of enzyme used for database searching. See showEnzyme.
xmx	Set for parameter of "Java -Xmx".
varmod	Variable modifications used for database searching. See showMods.
fixmod	Fixed modifications used for database searching. See showMods.
refine	Refine search, default is TRUE
ntt	Default is 1
tol	The error window on experimental peptide mass values
tolu	Units can be selected from: ppm, Daltons.
itol	Error window for MS/MS fragment ion mass values.
itolu	Units can be selected from: Daltons
miss	Max miss clevage

Value

a file path

Author(s)

Bo Wen [e-mail]

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