parserGear {sapFinder} | R Documentation |
This function is mainly for q-value calculation, protein inference and variant peptides spectra annotation.
parserGear(file = NULL, db = NULL, outdir = "parser_outdir", prefix = "sapFinder_test", mutPrefix = "VAR", decoyPrefix = "###REV###", alignment = 1, xmx = NULL, thread = 1)
file |
MS/MS search file. Currently, only XML format file of X!Tandem and DAT result of Mascot are supported. |
db |
A FASTA format database file used for MS/MS
searching. Usually, it is from the output of the function
|
outdir |
Output directory. |
prefix |
The prefix of output file. |
mutPrefix |
The prefix of variant peptides ID.
Default is "VAR". "VAR" is the prefix which used by
function |
decoyPrefix |
The prefix of decoy sequences ID.
Default is "###REV###". "###REV###" is the prefix which
used by function |
alignment |
0 or 1 to determine if peptide should be alignment or not. Default is 1. |
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. |
xmx |
The maximum Java heap size. The unit is "G". |
## Step 1. Variation-associated database construction vcf <- system.file("extdata/sapFinder_test.vcf", package="sapFinder") annotation <- system.file("extdata/sapFinder_test_ensGene.txt", package="sapFinder") refseq <- system.file("extdata/sapFinder_test_ensGeneMrna.fa", package="sapFinder") xref <- system.file("extdata/sapFinder_test_BioMart.Xref.txt", package="sapFinder") outdir <- "db_dir" prefix <- "sapFinder_test" db.files <- dbCreator(vcf=vcf, annotation=annotation, refseq=refseq, outdir=outdir, prefix=prefix,xref=xref) ## Step 2. MS/MS searching mgf.path <- system.file("extdata/sapFinder_test.mgf", package="sapFinder") fasta.path <- db.files[1] xml.path <- runTandem(spectra=mgf.path, fasta=fasta.path, outdir=".", tol=10, tolu="ppm", itol=0.1, itolu="Daltons") ## Step 3. Post-processing parserGear(file=xml.path, db=fasta.path, prefix=prefix, outdir="parser_outdir", alignment=1)