## ----message = FALSE---------------------------------------------------------- library(BRGenomics) ## ----------------------------------------------------------------------------- bfile <- system.file("extdata", "PROseq_dm6_chr4.bam", package = "BRGenomics") ## ----------------------------------------------------------------------------- ps_reads <- import_bam(bfile, mapq = 20, revcomp = TRUE, paired_end = FALSE) ps_reads ## ----------------------------------------------------------------------------- sum(score(ps_reads)) ## ----------------------------------------------------------------------------- reads_expanded <- import_bam(bfile, mapq = 20, revcomp = TRUE, field = NULL, paired_end = FALSE) ps_reads[1:8] reads_expanded[1:8] ## ----------------------------------------------------------------------------- length(reads_expanded) == sum(score(ps_reads)) ## ----------------------------------------------------------------------------- ps <- import_bam(bfile, mapq = 20, revcomp = TRUE, shift = -1, trim.to = "3p", paired_end = FALSE) ps ## ----collapse = TRUE---------------------------------------------------------- length(ps_reads) length(ps) ## ----collapse = TRUE---------------------------------------------------------- sum(score(ps)) == sum(score(ps_reads)) ## ----collapse = TRUE---------------------------------------------------------- isBRG(ps) ## ----eval=FALSE--------------------------------------------------------------- # # import bam, automatically applying processing steps for PRO-seq # ps <- import_bam_PROseq(bfile, mapq = 30, paired_end = FALSE) # # # separate strands, and make minus-strand scores negative # ps_plus <- subset(ps, strand == "+") # ps_minus <- subset(ps, strand == "-") # score(ps_minus) <- -score(ps_minus) # # # use rtracklayer to export bigWig files # export.bw(ps_plus, "~/Data/PROseq_plus.bw") # export.bw(ps_minus, "~/Data/PROseq_minus.bw") ## ----------------------------------------------------------------------------- # local paths to included bedGraph files bg.p <- system.file("extdata", "PROseq_dm6_chr4_plus.bedGraph", package = "BRGenomics") bg.m <- system.file("extdata", "PROseq_dm6_chr4_minus.bedGraph", package = "BRGenomics") import_bedGraph(bg.p, bg.m, genome = "dm6") ## ----------------------------------------------------------------------------- # local paths to included bigWig files bw.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)