# #——消息= FALSE --------------------------------------------------------- 库(BRGenomics ) ## ----------------------------------------------------------------------------- bfile < -系统。文件(“extdata”、“PROseq_dm6_chr4。bam”,包= " BRGenomics ") ## ----------------------------------------------------------------------------- ps_reads < - import_bam (bfile mapq = 20, revcomp = TRUE, paired_end = FALSE) ps_reads ## ----------------------------------------------------------------------------- (得分(ps_reads求和 )) ## ----------------------------------------------------------------------------- reads_expanded < - import_bam (bfile mapq = 20, revcomp = TRUE,字段=零,paired_end = FALSE) ps_reads [1:8] reads_expanded [1:8 ] ## ----------------------------------------------------------------------------- 长度(reads_expanded) = =(分数(ps_reads求和 )) ## ----------------------------------------------------------------------------- ps < - import_bam (bfile mapq = 20, revcomp = TRUE,转变= 1,修剪。=“3 p”,paired_end = FALSE) ps # #——崩溃= TRUE --------------------------------------------------------- 长度(ps_reads) (ps ) ## ---- 崩溃= TRUE --------------------------------------------------------- 总和(得分(ps)) = =(分数(ps_reads求和 )) ## ---- 崩溃= TRUE --------------------------------------------------------- isBRG (ps ) ## ---- eval = FALSE -------------------------------------------------------------- # # 进口bam,自动应用处理步骤pro - seq# ps <- import_bam_PROseq(bfile, mapq = 30, paired_end = FALSE) # # #分离链，并使负链分数为负# ps_plus <-子集(ps, strand == "+") # ps_minus <-子集(ps, strand == "-") # score(ps_minus) <- -score(ps_minus) # # #使用rtracklayer导出bigWig文件# export。bw(ps_plus， "~/Data/PROseq_plus.bw") #导出。bw(~ /数据/ PROseq_minus.bw ps_minus。 ") ## ----------------------------------------------------------------------------- # 本地路径包括bg bedGraph文件。P <- system。文件(“extdata”、“PROseq_dm6_chr4_plus。bedGraph"， package = "BRGenomics") bg。M <- system。文件(“extdata”、“PROseq_dm6_chr4_minus。bedGraph"， package = "BRGenomics") import_bedGraph(bg.;p, bg。米,基因组= "德国马克 ") ## ----------------------------------------------------------------------------- # 本地路径包括bw大佬文件。P <- system。file("extdata", "PROseq_dm6_chr4_plus.bw", package = "BRGenomics") bw.m <- system.file("extdata", "PROseq_dm6_chr4_minus.bw", package = "BRGenomics") import_bigWig(bw.p, bw.m, genome = "dm6") ## ----------------------------------------------------------------------------- ps_list <- lapply(1:6, function(i) ps[seq(i, length(ps), 6)]) names(ps_list) <- c("A_rep1", "A_rep2", "B_rep1", "B_rep2", "C_rep1", "C_rep2") ## ----------------------------------------------------------------------------- ps_list[1:2] names(ps_list) ## ----------------------------------------------------------------------------- mergeGRangesData(ps_list, ncores = 1) ## ----------------------------------------------------------------------------- merge_ps <- mergeGRangesData(ps_list[[1]], ps_list[[2]], ps, ncores = 1) merge_ps ## ---- collapse = TRUE--------------------------------------------------------- isBRG(merge_ps) ## ----------------------------------------------------------------------------- mergeReplicates(ps_list, ncores = 1)