# #——风格,呼应= FALSE,结果=“黑名单”- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - BiocStyle::减价()knitr:: opts_chunk设置(eval = TRUE) # #美元——loadlib,消息= FALSE,警告= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(电离)库(ggplot2)库(gridExtra) # #——readData eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # fast5files < -列表。文件(路径= " /道路/ /数据/”,模式= "。fast5美元”,full.names = TRUE) #的例子。摘要< - readFast5Summary (fast5files) # #——loadData - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(minionSummaryData)数据(s.typhi.rep1) # #——exampleData - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - s.typhi。rep1 # #——extractData1,警告= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - baseCalled (s.typhi.rep1) # #——extractData2,警告= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - baseCalled (s.typhi.rep1 [1:2]) # #——summaryPlots1 fig.height = 5, fig.width = 12.5, = FALSE dev =“png”,警告- - - - - p1 < - plotReadAccumulation (s.typhi.rep1) p2 < - plotActiveChannels (s.typhi.rep1)网格。安排(p1, p2, ncol = 2) # #——readCategories fig.height = 5, fig.width = 12.5, = FALSE dev = svg,警告- - - - - p1 < - plotReadCategoryCounts (s.typhi.rep1) p2 < - plotReadCategoryQuals (s.typhi.rep1)网格。安排(p1, p2, ncol = 2) # #——summaryPlots2 fig.height = 5, fig.width = 12.5, = FALSE dev =“png”,警告- - - - - p1 < - plotEventRate (s.typhi.rep1) p2 < - plotBaseProductionRate (s.typhi.rep1)网格。安排(p1, p2, ncol = 2) # #——numReads fig.height = 4.8, fig.width = 14.5, = FALSE dev = svg,警告- - - - - p1 < - layoutPlot (s.typhi。rep1属性=“nreads”) p2 < - layoutPlot (s.typhi。rep1属性= " kb)网格。安排(p1, p2, ncol = 2) # #——heatmapExample fig.height = 4.8, fig.width = 14.5, dev = svg,消息= FALSE,警告= FALSE——图书馆(dplyr) read_count_2D < - baseCalled (s.typhi.rep1) % > % # #从基础开始叫读取过滤器(链= =“模板”)% > % # #保持模板所以我们不计数的东西两次left_join (readInfo (s.typhi.rep1) =“id”) % > % # #通道存储在@readInfo槽匹配的id列group_by(频道)% > % # #集团根据频道总结(d2_count长度= ((full_2D = = TRUE)), # #数那些完全2 d地位d2_prop长度= ((full_2D = = TRUE)) / n()) # #除以总数量从通道读取# #情节并排p1 < - channelHeatmap (read_count_2D zValue = d2_count) p2 < - channelHeatmap (read_count_2D zValue = d2_prop)网格。安排(p1, p2, ncol = 2) # #——channelActivity fig.height = 4.8, fig.width = 10, dev = png,消息= FALSE,警告= FALSE - - - - -数据(s.typhi。rep3包= minionSummaryData) # #我们将阴谋事件信号中值为每个读在z轴z_scale =选择(eventData (s.typhi.rep3) id, median_signal) channelActivityPlot (s.typhi。rep3 zScale = z_scale) # #——pentamerCorrelation fig.height = 5, fig.width = 6.5, dev = png,消息= FALSE,警告= FALSE——plotKmerFrequencyCorrelation (s.typhi。rep3 only2D = FALSE) # #——combinedplots, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - p1 # < - channelActivityPlot (dat,选择(eventData (dat) id, median_signal)) # p2 < - plotKmerFrequencyCorrelation (dat) #网格。安排(p1, p2, ncol = 2) # #——writefastq,消息= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(ShortRead) writefastq (fastq (s.typhi。rep1)、文件= tempfile ()) # #——writefastq2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - writeFastq (fastq2D (s.typhi。rep1)、文件= tempfile ()) # #——fast5toFastq - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fast5files < -系统。文件(extdata,例子。fast5’,包= "电离”)fast5toFastq (= fast5files文件,文件名=“测试”,outputDir = tempdir()、链=‘所有’,ncores = 1)列表。文件(path = tempdir()模式= " * .fq.gz $ ")