parserGear {PGA} | R Documentation

## Post-processing for the identification result

### Description

This function is mainly for q-value calculation, protein inference and novel peptides spectra annotation.

### Usage

    parserGear(file = NULL, db = NULL, outdir = "parser_outdir",
      prefix = "pga", novelPrefix = "VAR", decoyPrefix = "###REV###",
      alignment = 1, xmx = NULL, thread = 1, msfile = NULL)

### Arguments

`file` | MS/MS search file. Currently, only XML format file of X!Tandem, DAT result of Mascot and mzIdentML result file (MS-GF+, MyriMatch, IPeak, OMSSA, ...) are supported.
`db` | A FASTA format database file used for MS/MS searching. Usually, it is from the output of the function `dbCreator`.
`outdir` | Output directory.
`prefix` | The prefix of output file.
`novelPrefix` | The prefix of novel protein ID. Default is "VAR". "VAR" is the prefix which used by function `dbCreator`. This value should be left to the default when your database is constructed by the function `getTrinityDB`.
`decoyPrefix` | The prefix of decoy sequences ID. Default is "###REV###". "###REV###" is the prefix which used by function `dbCreator`.
`alignment` | 0 or 1 to determine if peptide should be alignment or not. Default is 1.
`xmx` | The maximum Java heap size. The unit is "G".
`thread` | This parameter is used to specify the number of threads. "0" represents that all of the available threads are used; "1" represents one thread is used; "2" represents two threads are used,and so on. Default is 1.
`msfile` | The MS/MS data (mgf format) used.

### Value

none

### Examples

    vcffile <- system.file("extdata/input", "PGA.vcf",package="PGA")
    bedfile <- system.file("extdata/input", "junctions.bed",package="PGA")
    gtffile <- system.file("extdata/input", "transcripts.gtf",package="PGA")
    annotation <- system.file("extdata", "annotation",package="PGA")
    outfile_path<-"db/"
    outfile_name<-"test"
    library(BSgenome.Hsapiens.UCSC.hg19)
    dbfile <- dbCreator(gtfFile=gtffile,vcfFile=vcffile,bedFile=bedfile,
                        annotation_path=annotation,outfile_name=outfile_name,
                        genome=Hsapiens,outdir=outfile_path)

    msfile <- system.file("extdata/input", "pga.mgf",package="PGA")

    ## X!Tandem as the peptide identification software
    idfile <- runTandem(spectra = msfile, fasta = dbfile, outdir = "./", cpu = 6,
                        enzyme = "[KR]|[X]", varmod = "15.994915@M",itol = 0.05,
                        fixmod = "57.021464@C", tol = 10, tolu = "ppm",
                        itolu = "Daltons", miss = 2, maxCharge = 8, ti = FALSE)
    parserGear(file = idfile, db = dbfile, decoyPrefix="#REV#",xmx=1,thread=8,
               outdir = "parser_outdir")

    ## Mascot as the peptide identification software
    dat_file <- system.file("extdata/input", "mascot.dat",package="PGA")
    parserGear(file = dat_file, db = dbfile, decoyPrefix="#REV#",xmx=1,thread=8,
               outdir = "parser_outdir_mascot")

[Package PGA version 1.16.0 Index]