msQCpipe: The main function of msQC pipeline

In wenbostar/proteoQC: An R package for proteomics data quality control

Description

This function is designed to automate generating of target-decoy database, database searcing, post-processing and report generation.

Usage

msQCpipe(spectralist = NULL, fasta = "", outdir = "./", mode = "",
  miss = 2, enzyme = 1, varmod = NULL, fixmod = NULL, tol = 10,
  tolu = "ppm", itol = 0.6, itolu = "Daltons", threshold = 0.01,
  cpu = 0, xmx = 2, refine = TRUE, ntt = 1, ...)

Arguments

spectralist	A file contains the experiment design or a single mgf file
fasta	database file, must contain decoy sequences
outdir	output directory
mode	identification or quantification
miss	max miss clevage
enzyme	enzyme
varmod	Variable modifications are those which may or may not be present.
fixmod	Fixed modifications are applied universally, to every instance of the specified residue(s) or terminus.
tol	The error window on experimental peptide mass values
tolu	Units can be selected from: ppm, Daltons(also da or Da).
itol	Error window for MS/MS fragment ion mass values.
itolu	Units can be selected from: Daltons(also da or Da)
threshold	FDR value for PSM
cpu	Max number of cpu used
xmx	JAVA -Xmx
refine	Refine search for X!Tandem, default is TRUE.
ntt	Semi-tryptic, 1; fully-tryptic, 2.
...	Additional parameters passed to read.table used to read the experimental design.

Value

A list which contains all of the information for data quality report generating

Author(s)

Bo Wen [e-mail]

Examples

## Not run: 
library("rpx")
px <- PXDataset("PXD000864")
mgfs <- grep("mgf", pxfiles(px), value = TRUE)
mgfs <- grep("-0[5-6]-[1|2]", mgfs, value=TRUE)
mgffiles <- pxget(px, mgfs)
library("R.utils")
mgffiles <- sapply(mgffiles, gunzip)
## Generate the lightweight qc report, 
## trim the mgf files to 1/10 of their size.
trimMgf <- function(f, m = 1/10, overwrite = FALSE) {
  message("Reading ", f)
  x <- readLines(f)
  beg <- grep("BEGIN IONS", x)
  end <- grep("END IONS", x)
  n <- length(beg)
  message("Sub-setting to ", m)
  i <- sort(sample(n, floor(n * m)))
  k <- unlist(mapply(seq, from = beg[i], to = end[i]))
  if (overwrite) {
    unlink(f)
    message("Writing ", f)
    writeLines(x[k], con = f)
    return(f)
  } else {
    g <- sub(".mgf", "_small.mgf", f)
    message("Writing ", g)
    writeLines(x[k], con = g)
    return(g)
  }    
}
set.seed(1)
mgffiles <- sapply(mgffiles, trimMgf, overwrite = TRUE)
fas <- pxget(px, "TTE2010.zip")
fas <- unzip(fas)
design <- system.file("extdata/PXD000864-design.txt", package = "proteoQC")
read.table(design, header = TRUE)
qcres <- msQCpipe(spectralist = design,
                 fasta = fas, 
                 outdir = "./qc",
                 miss  = 0,
                 enzyme = 1, varmod = 2, fixmod = 1,
                 tol = 10, itol = 0.6, cpu = 2,
                 mode = "identification")

## End(Not run)

wenbostar/proteoQC documentation built on Nov. 20, 2020, 10:15 a.m.