# #——foo,包括= FALSE,回声= FALSE ------------- 选项(保持。源= TRUE,宽度= 48)foo < - packageDescription(“subSeq ") ## ---- load_subSeq ------------------------------ 库(subSeq)数据(锤)# #——download_hammer eval = FALSE -------------- # 负载(url(“http://bowtie-bio.sourceforge.net/recount/ExpressionSets/hammer_eset.RData”))#锤= hammer.eset # #——setup_hammer,取决于=“load_subSeq”——锤。counts = Biobase::exprs(hammer)[， 1:4] hammer.design = Biobase::pData(hammer)[1:4，] hammer。数量= hammer.counts [rowSums (hammer.counts) > = 5 , ] ## ---- 比例 ------------------------------ 比例= 10 ^ seq比例(2 0。5)# #——subSeq_example,取决于= c(“setup_hammer”、“比例”)——次级样本=子样品(锤。counts, ratios, method=c("edgeR"， "voomLimma")， treatment=hammer.design$protocol) ## ----show_subsamples, dependson="subSeq_edgeR"---- options(width=40) subsamples ## ----summary_subsamples, dependson="subSeq_edgeR"---- subsamples。Summary = Summary (subsamples)子样本。summary ## ----plot_subsamples, dependson="summary_subsamples"， echo=FALSE---- plot(subsamples.summary) ## ----custom_ggplot2, dependson="summary_subsamples"， out。身高= " 3 ",。宽度="3in"----库(ggplot2) ggplot(子样本。Summary, aes(x=depth, y=percent, col=method)) + geom_line() ## ----custom_ggplot2_2, dependson=c("summary_subsamples"， "custom_ggplot2")， out。身高= " 3 ",。宽度= " 3 "——ggplot(次级样本。summary, aes(x=深度，y=pearson, col=方法))+ geom_line() ## ----subsamples_myMethod, eval=FALSE---- # subsamples = subsample(锤子。counts, proportion, method=c("edgeR"， "DESeq2"， "myMethod")， treatment=hammer.design$protocol) ## ----subsamples_more, dependson="subSeq_example"---- seed = getSeed(subsamples) subsamples。更多= subsample(锤子。counts, ratios, method=c("voomLimma")， treatment =hammer.design$protocol, seed=seed) ## ----subsamples_more_combine, dependson="subsamples_more"---- subsamples.combined = combineSubsamples(subsamples, subsamples.more) plot(summary(subsamples.combined)) ## ---- generate_subsamples, dependson="subsamples_more"---- submatrix = generateSubsampledMatrix(hammer. more)计数，.1，种子=种子)dim(子矩阵)sum(子矩阵)