PGA (version 1.2.2)

parserGear: 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")