# #——风格,回声= FALSE,结果= '飞机 '----------------------------------- BiocStyle:减价 () ## ---- 设置中,回声= FALSE --------------------------------------------------- 选项(数字= 3)suppressPackageStartupMessages({库(csaw)库(磨边机)图书馆(GenomicRanges)图书馆(ChIPseeker)库(genefilter ) }) ## ---- null-p,缓存= TRUE -------------------------------------------------- ## 100000 t空下,n = 6 n < - 6;m <- matrix(rnorm(n * 100000)， ncol=n) P <- genefilter::rowttests(m, factor(rep(1:2，每个=3)))$ P。值分位数(P c(。001 . 01 . 05)嘘(P,减免= 20)# #——csaw-preprocess eval = FALSE ----------------------------------------- # 系统。文件(包= " UseBioconductor”、“脚本”,“ChIPSeq”、“NFYA preprocess.R #” ") ## ---- csaw-setup ---------------------------------------------------------- 文件< -本地({acc < - c (es_1 =“SRR074398 es_2 =“SRR074399 tn_1 =“SRR074417 tn_2 =“SRR074418”)data.frame(治疗=子 ("_.*", "", 名称(acc)),复制=子(“。*_"， ""，名称(acc))， sra=sprintf("%s。fastq=sprintf("% s.s fastq.gz"， acc)， bam=sprintf("% s.s fastq.gz.subread. ")BAM”,acc), row.names = acc, stringsAsFactors = FALSE ) }) ## ---- csaw-setwd eval = FALSE ---------------------------------------------- # setwd(“~ / UseBioconductor-data / ChIPSeq / NFYA ") ## ---- csaw-reduction eval = FALSE ------------------------------------------ # 库(csaw) #库(GenomicRanges) #碎片弹。len <- 110 #系统。# data <- windowCounts(files$bam, width=10, ext= fragl .len) #}) # 156秒# acc <- sub(".fastq. len ")*”、“”,数据bam.files美元)# colData(数据)< - cbind(文件(acc,), colData(数据 )) ## ---- csaw-filter eval = FALSE --------------------------------------------- # 图书馆(磨边机)# aveLogCPM() #保持< - aveLogCPM(分析(数据))> = 1 # < -数据保留 ,] ## ---- csaw-data-load,回声= FALSE ------------------------------------------ 碎片弹。len <- 110fl <-系统。文件(包=“UseBioconductor”、“extdata”、“csaw-data-filtered.Rds”)数据<——readRDS (fl) # #——csaw-normalize eval = FALSE ------------------------------------------ # 系统。time({ # binned <- windowCounts(files$bam, bin=TRUE, width=10000) # }) #139 second # normfacs <- normalize(binned) ## ----csaw-normacs-load, echo=FALSE--------------------------------------- fl <- system.file(package="UseBioconductor", "extdata", "csaw-normfacs.Rds") normfacs <- readRDS(fl) ## ----csaw-experimental-design-------------------------------------------- design <- model.matrix(~Treatment, colData(data)) ## ----csaw-de------------------------------------------------------------- y <- asDGEList(data, norm.factors=normfacs) y <- estimateDisp(y, design) fit <- glmQLFit(y, design, robust=TRUE) results <- glmQLFTest(fit, contrast=c(0, 1)) head(results$table) ## ----csaw-merge-windows-------------------------------------------------- merged <- mergeWindows(rowRanges(data), tol=1000L) ## ----csaw-combine-merged-tests------------------------------------------- tabcom <- combineTests(merged$id, results$table) head(tabcom) ## ----csaw-grangeslist---------------------------------------------------- gr <- rowRanges(data) mcols(gr) <- as(results$table, "DataFrame") grl <- split(gr, merged$id) mcols(grl) <- as(tabcom, "DataFrame")