# #——消息= FALSE ------------------------------------------------------------ 库(nullrangesData)国土安全部< - DHSA549Hg38 () ## ----------------------------------------------------------------------------- 库(nullranges ) ## ----------------------------------------------------------------------------- set.seed(5) #再现性库(微基准测试)blockLength < - 5 e5微基准测试(列表=船向一边倾斜的(p_within = bootRanges(国土安全部,blockLength = blockLength类型=“交换”,withinChrom = TRUE),b_within = bootRanges(国土安全部,blockLength = blockLength类型=“引导”,withinChrom = TRUE), p_across = bootRanges(国土安全部,blockLength = blockLength类型=“交换”,withinChrom = FALSE), b_across = bootRanges(国土安全部,blockLength = blockLength类型=“引导”,withinChrom = FALSE)),乘以= 10 ) ## ----------------------------------------------------------------------------- 库(GenomicRanges) seq_nms < -代表(c(“chr1”、“chr2”,“chr3”),c(4、5、2))gr < -农庄(seqnames = seq_nms IRanges(开始= c(1101121201年101201216231401, 1101),宽度= c(20 20 5、5、30日,5日,5日,5日,30日,80年,40)),seqlengths = c (chr1 = 300, chr2 = 450, chr3 = 200),装备(seq_nms =因素 )) ## ----------------------------------------------------------------------------- suppressPackageStartupMessages(图书馆(plotgardener)) plotGRanges < -函数(gr) {pageCreate(宽度= 5,高度= 2,xgrid = 0, ygrid = 0,showGuides = FALSE) for (i in seq_along(seqlevels(gr)) {chrom <- seqlevels(gr)[i] chromend <- seqlengths(gr)[[chrom]] suppressMessages({p <- pgParams(chromstart = 0, chromend = chromend, x = 0.5, width = 4*chromend/500, height = 0.5, at = seq(0, chromend, 50)， fill = colorby("chr"， palette=palette.colors)) prngs <- plotRanges(data = gr, params =p, chrom = chrom, y = 0.25 + (i-1)*.)7 = c(“左”、“底”))annoGenomeLabel(情节= prng params = p, y = 0.30 +(张)* 7 ) }) } } ## ---- toyranges fig.width = 5, fig.height = 2 ------------------------------------- plotGRanges (gr) # #——perm-within fig.width = 5, fig.height = 2 ----------------------------------- (我在1:2){gr_prime < - bootRanges (gr、blockLength = 100、类型=“交换”,withinChrom = TRUE) plotGRanges (gr_prime ) } ## ---- boot-within fig.width = 5,fig.height = 2 ----------------------------------- (我在1:2){gr_prime < - bootRanges (gr blockLength = 100, withinChrom = TRUE) plotGRanges (gr_prime ) } ## ---- perm-across fig.width = 5, fig.height = 2 ----------------------------------- (我在1:2){gr_prime < - bootRanges (gr、blockLength = 200、类型=“交换”,withinChrom = FALSE) plotGRanges (gr_prime ) } ## ---- boot-across fig.width = 5, fig.height = 2 ----------------------------------- (我在1:2){gr_prime < bootRanges (gr, blockLength = 200,plotGRanges (gr_prime withinChrom = FALSE) ) } ## ----------------------------------------------------------------------------- sessionInfo ()