easyRun {PGA} | R Documentation

## easyRun

### Description

This function is used to automate the peptide identification based on searching the customized database derived from RNA-Seq data.

### Usage

    easyRun(gtfFile = NULL, vcfFile = NULL, bedFile = NULL, spectra = NULL,
      annotation_path = NULL, outdir = "pga_dir", outPrefix = "pga",
      lablersid = FALSE, COSMIC = FALSE, bool_get_longest = TRUE,
      organism = "Homo sapiens", genome = NULL, enzyme = "[KR]|[X]",
      tol = 10, tolu = "ppm", itol = 0.6, itolu = "Daltons",
      varmod = NULL, fixmod = NULL, miss = 2, maxCharge = 8, ti = FALSE,
      cpu = 0, alignment = 1, xmx = 2, ...)

### Arguments

`gtfFile` | A GTF format file containing novel transcripts information
`vcfFile` | A VCF format file containing SNV and INDEL information
`bedFile` | A BED format file containing juction information
`spectra` | MS/MS peak list file
`annotation_path` | This directory contains numerous pieces of genome annotation information which can be downloaded by `PrepareAnnotationEnsembl2` or `PrepareAnnotationRefseq2`.
`outdir` | Output directory.
`outPrefix` | The prefix of output file.
`lablersid` | A logical indicating whether to do the SNV annotation(dbSNP)
`COSMIC` | A logical indicating whether to do the SNV annotation(COSMIC)
`bool_get_longest` | When it's set as TRUE, the longest sequences will be retained after the DNA sequences are six-frame translated into protein sequences. Otherwise, the protein sequences more than 30 aa are retained.
`organism` | What is the Genus and species of this organism.Please use proper scientific nomenclature for example: "Homo sapiens" and not "human", default is "Homo sapiens".
`genome` | Genome information. This is a BSgenome object(e.g. Hsapiens).
`enzyme` | Specification of specific protein cleavage sites. Default is "[KR]|[X]".
`tol` | Parent ion mass tolerance (monoisotopic mass).
`tolu` | Parent ion M+H mass tolerance window units.
`itol` | Fragment ion mass tolerance (monoisotopic mass).
`itolu` | Unit for fragment ion mass tolerance (monoisotopic mass).
`varmod` | Specificiation of potential modifications of residues.
`fixmod` | Specification of modifications of residues.
`miss` | The number of missed cleavage sites. Default is 2.
`maxCharge` | The Maximum parent charge, default is 8
`ti` | anticipate carbon isotope parent ion assignment errors. Default is false.
`cpu` | The number of CPU used for X!Tandem search. Default is 1.
`alignment` | 0 or 1 to determine if peptide should be alignment or not. Default is 0.
`xmx` | The maximum Java heap size. The unit is "G".
`...` | Additional arguments

### 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")
    library(BSgenome.Hsapiens.UCSC.hg19)
    msfile <- system.file("extdata/input", "pga.mgf",package="PGA")
    easyRun(gtfFile=gtffile,vcfFile=vcffile,bedFile=bedfile,spectra=msfile,
            annotation_path=annotation,genome=Hsapiens,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,xmx=1)

[Package PGA version 1.8.1 Index]