# #设置,eval = FALSE -------------------------------------------------------- # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) # install.packages (BiocManager) # BiocManager::安装(“SeqSQC ") ## ---- 加载包 ------------------------------------------------------------ 库(SeqSQC) # #——loadData eval = TRUE ------------------------------------------------------ infile < -系统。文件(“extdata”、“example_sub。vcf”,包= " SeqSQC样品”)。annot < -系统。file("extdata"， "sampleAnnotation.txt"， package="SeqSQC")文件(“extdata”、“CCDS.Hs37.3.reduced_chr1。bed"， package="SeqSQC") outdir <- tempdir() outfile <- file。路径(testWrapUp outdir。 ") ## ---- wrapup_vcf eval = FALSE --------------------------------------------------- # seqfile < - sampleQC (vfile = infile、输出=输出文件,截图所示。Region = cr，样本。annot =样本。annot,格式。data = "NGS"，格式。文件= " vcf " QCreport = FALSE) #保存(seqfile、文件= " seqfile.RData ") ## ---- wrapup_seqfile eval = FALSE ----------------------------------------------- # 负载(系统。文件(“extdata”、“example.seqfile。Rdata"， package="SeqSQC")) # gfile <- system. .文件(“extdata”、“例子。gds"， package="SeqSQC") # seqfile <- SeqSQC(gdsfile = gfile, QCresult = QCresult(seqfile))) ## seqfile <- sampleQC(vfile = seqfile, output =" testWrapUp"， QCreport =TRUE) # save(seqfile, file="seqfile. rdata ") ## ----loadVfile, eval=TRUE, message=FALSE-------------------------------------- seqfile <- loadVfile (vfile = infile, output = outfile, capture. txt)Region = cr，样本。annot =样本。annot) ## ----show--------------------------------------------------------------------- load(system.file("extdata", "example.seqfile.Rdata", package="SeqSQC")) gfile <- system.file("extdata", "example.gds", package="SeqSQC") seqfile <- SeqSQC(gdsfile = gfile, QCresult = QCresult(seqfile)) slotNames(seqfile) ## ----class-------------------------------------------------------------------- gdsfile(seqfile) ## ----class2------------------------------------------------------------------- QCresult(seqfile) head(QCresult(seqfile)$sample.annot) ## ----gds---------------------------------------------------------------------- showfile.gds(closeall=TRUE) dat <- SeqOpen(seqfile) dat closefn.gds(dat) ## ----missingrate, eval=FALSE-------------------------------------------------- # seqfile <- MissingRate(seqfile, remove.samples=NULL) ## ----mrresult, eval=TRUE------------------------------------------------------ res.mr <- QCresult(seqfile)$MissingRate tail(res.mr) ## ----plot.mr------------------------------------------------------------------ plotQC(seqfile, QCstep = "MissingRate") ## ----sexcheck, eval=FALSE----------------------------------------------------- # seqfile <- SexCheck(seqfile, remove.samples=NULL) ## ----scresult, eval=TRUE------------------------------------------------------ res.sexc <- QCresult(seqfile)$SexCheck tail(res.sexc) ## ----plot.sexc---------------------------------------------------------------- plotQC(seqfile, QCstep = "SexCheck") ## ----inbreeding, eval=FALSE--------------------------------------------------- # seqfile <- Inbreeding(seqfile, remove.samples=NULL) ## ----inbresult, eval=TRUE----------------------------------------------------- res.inb <- QCresult(seqfile)$Inbreeding tail(res.inb) ## ----plot.inb----------------------------------------------------------------- plotQC(seqfile, QCstep = "Inbreeding") ## ----ibd, eval=FALSE---------------------------------------------------------- # seqfile <- IBD(seqfile, remove.samples=NULL) ## ----ibdresult, eval=TRUE----------------------------------------------------- res.ibd <- QCresult(seqfile)$IBD head(res.ibd) ## ----plot.ibd----------------------------------------------------------------- plotQC(seqfile, QCstep = "IBD") ## ----pca, eval=FALSE---------------------------------------------------------- # seqfile <- PCA(seqfile, remove.samples=NULL) ## ----pcaresult, eval=TRUE----------------------------------------------------- res.pca <- QCresult(seqfile)$PCA tail(res.pca) ## ----plot.pca----------------------------------------------------------------- plotQC(seqfile, QCstep = "PCA") ## ----plot.pca.inter, eval=TRUE, warning=FALSE--------------------------------- plotQC(seqfile, QCstep = "PCA", interactive=TRUE) ## ----problist----------------------------------------------------------------- problemList(seqfile) save(seqfile, file="seqfile.Rdata") ## ----report, eval=FALSE------------------------------------------------------- # RenderReport(seqfile, output="report.html", interactive=TRUE) ## ----------------------------------------------------------------------------- sessionInfo()