easyRun

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Description

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

Usage

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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

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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)