## ----style, eval=TRUE, echo=FALSE, results='asis'-------------------------- BiocStyle::latex() ## ----env, echo=FALSE,warning=FALSE,message=FALSE--------------------------- suppressPackageStartupMessages(library("PGA")) #suppressPackageStartupMessages(library("R.utils")) ## ----bdb, eval=TRUE, warning=FALSE, message=FALSE, cache=TRUE-------------- 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") outfile_path<-"db/" outfile_name<-"test" library(BSgenome.Hsapiens.UCSC.hg19) dbfile <- dbCreator(gtfFile=gtffile,vcfFile=vcffile,bedFile=bedfile, annotation_path=annotation,outfile_name=outfile_name, genome=Hsapiens,outdir=outfile_path) ## ----denovo, echo=TRUE, cache=FALSE, tidy=FALSE,eval=TRUE, warning=FALSE---- transcript_seq_file <- system.file("extdata/input", "Trinity.fasta", package="PGA") outdb <- createProDB4DenovoRNASeq(infa=transcript_seq_file, outfile_name = "denovo") cat(outdb,"\n") ## ----databasesearching, echo=TRUE, cache=TRUE, tidy=FALSE,eval=TRUE,warning=FALSE---- msfile <- system.file("extdata/input", "pga.mgf",package="PGA") idfile <- runTandem(spectra = msfile, fasta = dbfile, outdir = "./", 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) ## ----parserGear, echo=TRUE, cache=TRUE, tidy=FALSE, eval=TRUE, warning=FALSE, message=FALSE---- parserGear(file = idfile, db = dbfile, decoyPrefix="#REV#",xmx=1,thread=8, outdir = "parser_outdir") ## ----mascotParser, eval=TRUE, echo=TRUE, cache=TRUE, tidy=FALSE, warning=FALSE, message=FALSE---- dat_file <- system.file("extdata/input", "mascot.dat",package="PGA") parserGear(file = dat_file, db = dbfile, decoyPrefix="#REV#",xmx=1,thread=8, outdir = "parser_outdir_mascot") ## ----parsermzid, eval=FALSE, echo=TRUE, cache=TRUE, tidy=FALSE, warning=FALSE, message=FALSE---- # ## The following code works only after the java parser has been updated. # 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") # outfile_path<-"db/" # outfile_name<-"test" # library(BSgenome.Hsapiens.UCSC.hg19) # dbfile <- dbCreator(gtfFile=gtffile,vcfFile=vcffile,bedFile=bedfile, # annotation_path=annotation,outfile_name=outfile_name, # genome=Hsapiens,outdir=outfile_path) # # msfile <- system.file("extdata/input", "pga.mgf",package="PGA") # # ## MS-GF+ (mzIdentML) as the peptide identification software # mzid <- system.file("extdata/input", "msgfplus.mzid",package="PGA") # parserGear(file = mzid, db = dbfile, msfile = msfile, # decoyPrefix="#REV#",xmx=1,thread=8, # outdir = "parser_outdir") ## ----reportg, echo=TRUE, cache=TRUE, tidy=FALSE, eval=TRUE, warning=FALSE, message=FALSE---- reportGear(parser_dir = "parser_outdir", tab_dir = outfile_path, report_dir = "report") ## ----addGeneName4Ensembl,echo=TRUE, cache=TRUE, tidy=FALSE, eval=FALSE, warning=FALSE, message=FALSE---- # # ## Don't run. It only works if you have generated a # ## report with using Ensembl annotation. # mart <- biomaRt::useMart("ENSEMBL_MART_ENSEMBL", # dataset="hsapiens_gene_ensembl", # host="grch37.ensembl.org", # path="/biomart/martservice", # archive=FALSE) # # addGeneName4Ensembl(mart=mart,report="report") ## ----auto, echo=TRUE, cache=TRUE, tidy=FALSE, eval=TRUE, warning=FALSE, message=FALSE---- 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) ## ----sessioninfo, results='asis', echo=FALSE------------------------------- toLatex(sessionInfo())