# #设置,包括= FALSE --------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) ## ---- fig.cap =“婴儿车工作流”。宽度= 237 px,。身高= 233 px,回声= F——knitr:: include_graphics(“workflow_noScreen.jpg ") ## ---- installFromGitHub eval = FALSE -------------------------------------------- # devtools:: install_github (' pliu55 /婴儿车 ') ## ---- installFromBioconductor eval = FALSE -------------------------------------- # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) # install.packages (BiocManager) # BiocManager::安装(“婴儿车 ") ## ---- runQuickPRAM eval = FALSE ------------------------------------------------- # ## # ## 假设stringtie二进制文件在文件夹/usr/local/stringtie-1.3.3 / # # # #婴儿车::runPRAM (in_gtf、in_bamv out_gtf,方法=“plst”,# stringtie = / usr /中心/ stringtie-1.3.3 / stringtie ') ## ---- accessExample ------------------------------------------------------------ 执行(“extdata /演示/。gtf婴儿车,包= ') ## ---- runPRAM eval = FALSE ------------------------------------------------------ # in_gtf =执行(“extdata /演示/。gtf `， package='pram') # # in_bamv = c(system.file('extdata/demo/SZP. file ')# system.file('extdata/demo/TLC. bat '， package='pram')， # system.file('extdata/demo/TLC. bat ')bam,包= '婴儿车'))# # pred_out_gtf = tempfile (fileext = ' .gtf ') # # ## # ## 假设stringtie二进制文件在文件夹/usr/local/stringtie-1.3.3 / # # # #婴儿车::runPRAM (in_gtf、in_bamv pred_out_gtf,方法=“plst”,# stringtie = / usr /中心/ stringtie-1.3.3 / stringtie ') ## ---- 回声= F ------------------------------------------------------------------- defIgRanges url_hg19_chromsize = ' http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz ' # #,警告= FALSE ----------------------------------------------- 婴儿车::defIgRanges(执行(“extdata / gtf / defIgRanges_in。gtf’,包= '婴儿车hg38)基因组= ') ## ---- prepIgBam ---------------------------------------------------------------- finbam =执行(“extdata / bam / CMPRep2.sortedByCoord.raw。砰’,包= '婴儿车')iggrs = GenomicRanges:农庄(chr10:77236000 - 77247000: +) foutbam = tempfile (fileext =‘本’)婴儿车::prepIgBam (finbam、iggrs foutbam) # #——回声= F ------------------------------------------------------------------- url_cf_web = paste0(“(袖扣,Cuffmerge)”、“(http://cole-trapnell-lab.github.io/cufflinks/)”)url_cf_lnx = paste0(“(v2.2.1)”、“(http://cole-trapnell-lab.github。io/cufflinks/assets/'， 'downloads/cufflinks- 2.2.1.linux_x86_64 .tar.gz)') url_cf_mac = paste0('[v2.1.1]'， '(http://cole-trapnell-lab.github。io /袖扣/资产/”、“下载/ cufflinks-2.1.1.OSX_x86_64.tar.gz)”)cf_methods =“__plcf__ __cfmg__, __cftc__,和__cf__ ' url_st_web = paste0(“[StringTie, StringTie-merge]”,“(https://ccb.jhu.edu/software/stringtie/)”)url_st_lnx = paste0(“[v1.3.3b]”,“(http://ccb.jhu.edu/software/stringtie/dl/ ', ' stringtie-1.3.3b.Linux_x86_64.tar.gz)”)url_st_mac = paste0(“[v1.3.3b]”,“(http://ccb.jhu.edu/software/stringtie/dl/ ', ' stringtie-1.3.3b.OSX_x86_64.tar.gz)”)st_methods = ' __plst__, __stmg__,和__st__ url_tc_web = ' [TACO] (https://tacorna.github.io) ' url_tc_lnx = paste0(“[v0.7.0]”,“(https://github.com/tacorna/taco/releases/download/”、“v0.7.0 / taco-v0.7.0.Linux_x86_64.tar.gz)”)url_tc_mac = paste0(“(v0.7.0)”、“(https://github.com/tacorna/taco/releases/download/”、“v0.7.0 / taco-v0.7.0.OSX_x86_64.tar.gz )') ## ---- buildModel eval = FALSE --------------------------------------------------- # fbams = c(执行(“extdata / bam / CMPRep1.sortedByCoord.clean。bam'， # package='pram')， # system.file('extdata/bam/ cmppre2 . sortedbycord .clean. exe ')。bam”,#包=“婴儿车”)# # foutgtf = tempfile (fileext = ' .gtf ') # # ## # ## 假设stringtie二进制文件在文件夹/usr/local/stringtie-1.3.3 / # # # #婴儿车::buildModel (fbams、foutgtf方法=“plst”,# stringtie = / usr /中心/ stringtie-1.3.3 / stringtie ') ## ---- selModel ----------------------------------------------------------------- fin_gtf =执行(“extdata / gtf / selModel_in。gtf’,包= '婴儿车')fout_gtf = tempfile (fileext = .gtf)婴儿车::selModel (fin_gtf fout_gtf) # #——evalModel ---------------------------------------------------------------- fmdl =执行(“extdata /基准/体现。Tsv '， package='pram') FTGT = system.file('extdata/benchmark/tgt. file ')Tsv '， package='pram') MDLDT =数据。table::fread(fmdl, header=TRUE, sep="\t") tgtdt = data.table::fread(ftgt, header=TRUE, sep="\t") pram::evalModel(mdldt, tgtdt) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()