## ----风格，echo = false，结果='Asis'--------------------------------- Biocstyle :: Markdown（）选项（max.print = 1000）suppressPackageStartUpMessages（{库（Genefilter）库（Airway）库（Deseq2）库（基因组）库（基因组法）}）## ----睡眠。测试 - - - - - - - - - - - - - - - - - - - - - - - ---------头（睡眠）情节（额外〜组，数据=睡眠）##传统接口（睡眠，T.Test（额外[Group == 1]，额外[Group == 2]））##公式界面T.Test（额外〜组，睡眠）##组之间的等方差，t.test（额外〜组，睡眠，var.equal = true）## ----睡眠-LM -------------------------------------------------------------------------- ##线性模型;与t.test（var.equal = true）fit < - lm（extra〜group，睡眠）Anova（适合）## ---- Sleep-Model.matrix ------------------------------------------------ ##基础模型，用于`lm.fit（）`model.matrix（extra〜group，睡眠）＃last列表示组效果model.matrix（额外〜0 +组，睡眠）＃thearss ## ----睡眠 - 差异------------------------------------------------------------------------ FIT0 < - LM（额外〜ID，睡眠）FIT1 < - LM（额外〜ID +组，睡眠）ANOVA（FIT0，FIT1）T.Test（额外〜组，睡眠，var.equal = true，配对= true）## ---- Airway-BAM路径-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------图书馆（Airway）Path < - System.file（包=“Airway”，“ExtData”）DIR（路径）## ---- Airway-CSV-------------------------------------------------------------------------- csvfile < - dir（path，sample_table.csv“，full = true）采样< - read.csv（csvfile，row.names = 1）头（采样）## ----气道-bam ---------------------------------------------------------图书馆（RSAMTOOLS）文件名<- dir（path，“.bam $”，full = true）bamfiles < - bamfilelist（文件名，faigenamesize = 1000000）名称（Bamfiles）< - 子（“_ subset.bam”，“”，basename（filenames））## ----airway-gtf-to-txdb-------------------------------------------------- library(GenomicFeatures) gtffile <- file.path(path, "Homo_sapiens.GRCh37.75_subset.gtf") txdb <- makeTxDbFromGFF(gtffile, format="gtf", circ_seqs=character()) genes <- exonsBy(txdb, by="gene") ## ------------------------------------------------------------------------ library(GenomicAlignments) se <- summarizeOverlaps(features=genes, reads=bamfiles, mode="Union", singleEnd=FALSE, ignore.strand=TRUE, fragments=TRUE) colData(se) <- as(sampleTable, "DataFrame") se colData(se) rowData(se) head(assay(se)) ## ----airway-data--------------------------------------------------------- data(airway) se <- airway ## ----airway-cell-dex----------------------------------------------------- colData(se) ## ----airway-DESeq2-design------------------------------------------------ library(DESeq2) dds <- DESeqDataSet(se, design = ~ cell + dex) dds <- DESeq(dds) res <- results(dds) ## ----plotcounts, fig.width=5, fig.height=5------------------------------- topGene <- rownames(res)[which.min(res$padj)] res[topGene,] plotCounts(dds, gene=topGene, intgroup=c("dex")) ## ----plotma-------------------------------------------------------------- plotMA(res, ylim=c(-5,5)) ## ----airway-DESeq2-hist-------------------------------------------------- hist(res$pvalue, breaks=50) ## ----airway-DESeq2-volcano----------------------------------------------- plot(-log10(padj) ~ log2FoldChange, as.data.frame(res), pch=20)