Description Usage Arguments Value Examples
This function is used to automate the peptide identification based on searching the customized database derived from RNA-Seq data.
1 2 3 4 5 6 7 | 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, ...)
|
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
|
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 |
none
1 2 3 4 5 6 7 8 9 10 11 | 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)
|
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