# #设置,包括= FALSE,缓存= FALSE ----------------------------------- 要求(knitr) #组全球美元opts_chunk设置块选项(无花果。path='tmp/deepSNV-'， fig.align='center'， fig.show='hold'， fig.width=4, fig.height=4, out.width='。4 \ \线宽”,dpi = 150)选项(replace.assign = TRUE,宽度= 75)美元knit_hooks设置(好=函数(之前,选择,envir){如果(前)标准(mar = c(4 4。1。1)mgp = c(2.5, 1,0),电池= " n ") }) ## ---- = ' asis呼应= FALSE,结果 '------------------------------------------ 打印(引用(“deepSNV”)[1],风格= "乳胶 ") ## ------------------------------------------------------------------------ 库(deepSNV)地区< data.frame(=“B.FR.83.HXB2_LAI_IIIB_BRU_K034”,从而向开始= 2074,停止= 3585 ) ## ------------------------------------------------------------------------ # HIVmix < - deepSNV(测试= " http://www.bsse.ethz.ch/cbg/software/deepSNV/data/test.bam ", #控制= " http://www.bsse.ethz.ch/cbg/software/deepSNV/data/control.bam ", #区域=区域,q = 10 ) ## ------------------------------------------------------------------------ 数据(HIVmix) #附加数据相反,因为它可以在常规检查没有网络连接失败。表演(HIVmix ) ## ------------------------------------------------------------------------ 控制(HIVmix) [100:110] (HIVmix)[100:110测试 ,] ## ---- 艾滋病毒,好= TRUE ------------------------------------------------------ 情节(HIVmix ) ## ------------------------------------------------------------------------ SNVs < -总结(HIVmix sig.level = 0.05,adjust.method =“黑洞”)负责人(SNVs) nrow SNVs min (SNVs freq.var美元 ) ## ------------------------------------------------------------------------ 总和(RF(测试(HIVmix),总= T) > 0.01 &射频(测试(HIVmix),总= T) < 0.95 ) ## ------------------------------------------------------------------------ 数据(trueSNVs包=“deepSNV”)表(p.adjust (p.val (HIVmix)方法=“黑洞”)< 0.05,trueSNVs) # #——phiX dev =“jpeg”,好= TRUE ----------------------------------------- ## 加载数据(非规范)数据(phiX,包= " deepSNV”)情节(phiX cex.min = 5) # #规范化数据phiN <——正常化(phiX而圆= TRUE)情节(phiN cex.min = 5) # #——pval好= TRUE ----------------------------------------------------- p.norm < - p.val (phiN) n < - sum (! is.na (p.norm)) qqplot (p。规范,seq (1 / n 1 length.out = n),日志=“xy”=“S”型,xlab =“假定值”,ylab =“提供”)p.val <——p.val (phiX)点(排序(p.val [! is.na (p.val)]), seq (1 / n 1 length.out = n), pch = 16,坳=“灰色”=“S”型,lty = 2)传说(“topleft”,c(“原始数据”、“规范化数据”),pch = 16,坳= c(“灰色”、“黑色”),电池=“n”,lty = 3) abline (0, 1) # # - dev =“jpeg”,好= TRUE ----------------------------------------------- 数据(“碾压混凝土”,包=“deepSNV”)显示(RCC)情节碾压混凝土(RCC cex.min = 5)。bb = estimateDispersion(RCC, alternative="two.sided") plot(RCC. side)bb, cex.min = 5 ) ## ------------------------------------------------------------------------ RCC.bb@log.lik RCC@log.lik RCC.bb@log.lik - RCC@log.lik日志(4 * nrow(测试(碾压混凝土 ))) ## ------------------------------------------------------------------------ 总结(RCC adjust.method = " bonferroni”)[1:6 ] ## ------------------------------------------------------------------------ 标签< -总结(碾压混凝土。bb, adjust.method =“bonferroni”)[1:6]标签# #——回声= FALSE,结果= '飞机 '------------------------------------------ toLatex (sessionInfo ())