## ----style, echo = FALSE, results = 'asis'------------------------------------ library(BiocStyle) markdown(css.files = c('custom.css')) ## ----extraload,include = FALSE,echo = FALSE,eval = TRUE----------------------- library(dplyr,quietly = TRUE) library(BiocParallel) library(gridExtra) library(ChIPexoQual) library(ChIPexoQualExample) library(knitr) opts_chunk$set(fig.align = "center") ## ----load,include=TRUE,echo=TRUE,eval=FALSE----------------------------------- # # library(ChIPexoQual) # library(ChIPexoQualExample) # ## ----ex1,include=TRUE,echo=TRUE,eval=TRUE------------------------------------- files = list.files(system.file("extdata", package = "ChIPexoQualExample"),full.names = TRUE) basename(files[1]) ex1 = ExoData(file = files[1],mc.cores = 2L,verbose = FALSE) ex1 reads = readGAlignments(files[1],param = NULL) ex2 = ExoData(reads = reads,mc.cores = 2L,verbose = FALSE) identical(GRanges(ex1),GRanges(ex2)) ## ----pre_create,include=FALSE,echo=FALSE,eval = TRUE-------------------------- rm(reads,ex1,ex2) ## ----create_exdata,include=TRUE,echo=TRUE,eval=TRUE--------------------------- files = files[grep("bai",files,invert = TRUE)] ## ignore index files exampleExoData = lapply(files,ExoData,mc.cores = 2L,verbose = FALSE) ## ----depth,include=TRUE,echo=TRUE,eval=TRUE----------------------------------- sapply(exampleExoData,nreads) ## ----ARC1,include=TRUE,echo=TRUE,eval=TRUE,warning=FALSE,fig.height=4,fig.width=9,results='markup'---- ARCvURCplot(exampleExoData,names.input = paste("Rep",1:3,sep = "-")) ## ----strand1,include=TRUE,echo=TRUE,eval=TRUE,warning=FALSE,results="markup",fig.height=4---- p1 = regionCompplot(exampleExoData,names.input = paste("Rep",1:3, sep = "-"),depth.values = seq_len(50)) p2 = FSRDistplot(exampleExoData,names.input = paste("Rep",1:3,sep = "-"), quantiles = c(.25,.5,.75),depth.values = seq_len(100)) gridExtra::grid.arrange(p1,p2,nrow = 1) ## ----ARC2,include=TRUE,echo=TRUE,eval=TRUE,warning=FALSE,fig.height=4,fig.width=9,results='markup'---- ARCvURCplot(exampleExoData[[1]], subset(exampleExoData[[1]],uniquePos > 10), subset(exampleExoData[[1]],uniquePos > 20), names.input = c("All", "uniquePos > 10", "uniquePos > 20")) ## ----param_dist,include=TRUE,echo=TRUE,eval=TRUE,warning=FALSE,results="markup",fig.height=2.5---- p1 = paramDistBoxplot(exampleExoData,which.param = "beta1", names.input = paste("Rep",1:3,sep = "-")) p2 = paramDistBoxplot(exampleExoData,which.param = "beta2", names.input = paste("Rep",1:3,sep = "-")) gridExtra::grid.arrange(p1,p2,nrow = 1) ## ----param_eval,include=TRUE,echo=TRUE,eval=TRUE------------------------------ sapply(exampleExoData,function(x)median(beta1(x))) sapply(exampleExoData,function(x)median(-beta2(x))) ## ----subsamping,include=TRUE,echo=TRUE,eval=TRUE------------------------------ sample.depth = seq(1e5,2e5,5e4) exoList = ExoDataSubsampling(file = files[3],sample.depth = sample.depth, verbose=FALSE) ## ----subsamplots,include=TRUE,echo=TRUE,eval=TRUE,warning=FALSE,results="markup",fig.height=2.5---- p1 = paramDistBoxplot(exoList,which.param = "beta1") p2 = paramDistBoxplot(exoList,which.param = "beta2") gridExtra::grid.arrange(p1,p2,nrow = 1) ## ----info,include=TRUE,echo =TRUE,eval=TRUE----------------------------------- sessionInfo("ChIPexoQual")