easyRun: easyRun

In PGA: An package for identification of novel peptides by customized database derived from RNA-Seq

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)

PGA documentation built on Nov. 8, 2020, 6:20 p.m.