msQCpipe {proteoQC} | R Documentation

## The main function of msQC pipeline

### 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 wenbo@genomics.cn

### 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)

[Package proteoQC version 1.21.0 Index]