reportCreator {sapFinder} | R Documentation |
This function is used for HTML-based report writing
reportCreator(indir = ".", outdir = .REPORT.DIR, db = NULL, prefix = NULL, varInfor = NULL)
indir |
The directory of output files of function
|
outdir |
Output directory for this report |
db |
A FASTA format database file used for MS/MS
searching. Usually, it is from the output of the function
|
prefix |
It must be set the same with the parameter
of "prefix" in function |
varInfor |
It is a tab-delimited file contains
detailed variation information and is from the output of
the function |
## 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") ## Step 4. HTML-based report generation reportCreator(indir="parser_outdir", outdir="report", db=fasta.path, prefix=prefix, varInfor=db.files[2])