# #——风格,eval = TRUE,呼应= FALSE,结果=“黑名单”- - - - - - - - - - - - - - - - - - - - - - - - - - - - BiocStyle::乳胶()# # - - - - - env,呼应= FALSE,警告= FALSE,消息= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - suppressPackageStartupMessages(库(PGA)) # suppressPackageStartupMessages(库(“R.utils”)) # #——bdb, eval = TRUE,警告= FALSE,消息= FALSE,缓存= TRUE - - - - - - - - - - - - - - - - vcffile < -系统。文件(“extdata /输入”、“PGA.vcf”包= PGA) bedfile < -系统。文件(“extdata /输入”、“junctions.bed”包= PGA) gtffile < -系统。文件(“extdata /输入”、“transcripts.gtf”包= PGA)注释< -系统。文件(“extdata”、“注释”,包= PGA) outfile_path < - db /“outfile_name < -“测试”图书馆(BSgenome.Hsapiens.UCSC.hg19) dbfile <——dbCreator (gtfFile = gtfFile vcfFile = vcfFile bedFile = bedFile annotation_path =注释,outfile_name = outfile_name基因组= Hsapiens outdir = outfile_path) # #——从头,呼应= TRUE,缓存= FALSE,整洁= FALSE, eval = TRUE,警告= FALSE——transcript_seq_file < -系统。文件(“extdata /输入”、“三一。fasta”,包= PGA) outdb <——createProDB4DenovoRNASeq (infa = transcript_seq_file outfile_name =“重新”)猫(outdb,“\ n”) # #——databasesearching,呼应= TRUE,缓存= TRUE,整洁= FALSE, eval = TRUE,警告= FALSE——msfile < -系统。文件(“extdata /输入”、“pga.mgf”包= PGA) idfile < runTandem(光谱= msfile fasta = dbfile outdir = "。酶= " / ",cpu = 6日(KR) | [X]”, varmod = " 15.994915 @m”itol = 0.05, fixmod = " 57.021464 @c”,托尔= 10,妥鲁香胶= " ppm”, itolu =“道尔顿”= 2小姐maxCharge = 8, ti = FALSE) # #——parserGear,呼应= TRUE,缓存= TRUE,整洁= FALSE, eval = TRUE,警告= FALSE,消息= FALSE——parserGear(文件= idfile、db = dbfile decoyPrefix =“# #”牧师,xmx = 1,线程= 8,outdir =“parser_outdir”) # #——mascotParser, eval = TRUE,呼应= TRUE,缓存= TRUE,整洁= FALSE,警告= FALSE,消息= FALSE——dat_file < -系统。文件(“extdata /输入”、“mascot.dat”包= PGA) parserGear(文件= dat_file、db = dbfile decoyPrefix =“# #”牧师,xmx = 1,线程= 8,outdir =“parser_outdir_mascot”) # #——parsermzid, eval = FALSE,呼应= TRUE,缓存= TRUE,整洁= FALSE,警告= FALSE,消息= FALSE - - - - - # # #下面的代码只能在java解析器已经更新。# vcffile < -系统。文件(“extdata /输入”、“PGA.vcf”包= PGA) # bedfile < -系统。文件(“extdata /输入”、“junctions.bed”包= PGA) # gtffile < -系统。文件(“extdata /输入”、“transcripts.gtf”包= PGA) #注释< -系统。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())