## ----knitr, echo=FALSE, results="hide"---------------------------------------- library("knitr") opts_chunk$set(tidy=FALSE,dev="png",fig.show="hide", fig.width=4,fig.height=4.5, message=FALSE) ## ----style, eval=TRUE, echo=FALSE, results="asis"-------------------------- BiocStyle::latex() ## ----include=FALSE--------------------------------------------------------- library(knitr) opts_chunk$set( concordance=TRUE ) ## ----options, results="hide", echo=FALSE-------------------------------------- options(digits=3, width=80, prompt=" ", continue=" ") ## ----inputdata, eval=TRUE----------------------------------------------------- library(tracktables) fileLocations <- system.file("extdata",package="tracktables") bigwigs <- dir(fileLocations,pattern="*.bw",full.names=TRUE) intervals <- dir(fileLocations,pattern="*.bed",full.names=TRUE) bigWigMat <- cbind(gsub("_Example.bw","",basename(bigwigs)), bigwigs) intervalsMat <- cbind(gsub("_Peaks.bed","",basename(intervals)), intervals) FileSheet <- merge(bigWigMat,intervalsMat,all=TRUE) FileSheet <- as.matrix(cbind(FileSheet,NA)) colnames(FileSheet) <- c("SampleName","bigwig","interval","bam") SampleSheet <- cbind(as.vector(FileSheet[,"SampleName"]), c("EBF","H3K4me3","H3K9ac","RNAPol2"), c("ProB","ProB","ProB","ProB")) colnames(SampleSheet) <- c("SampleName","Antibody","Species") ## ----head_samplesheet, eval=TRUE---------------------------------------------- head(SampleSheet) ## ----head_filesheet, eval=FALSE----------------------------------------------- # head(FileSheet) ## ----Filesheet, eval=TRUE,echo=FALSE------------------------------------------ FileSheetEdited <- FileSheet FileSheetEdited[,2] <- file.path("pathTo",basename(FileSheetEdited[,2])) FileSheetEdited[1,3] <- file.path("pathTo",basename(FileSheetEdited[1,3])) head(FileSheetEdited) ## ----IGVsessionAndSample, eval=FALSE------------------------------------------ # # MakeIGVSession(SampleSheet,FileSheet,igvdirectory=getwd(),"Example","mm9") ## ----maketracktable, eval=FALSE----------------------------------------------- # HTMLreport <- maketracktable(fileSheet=FileSheet, # SampleSheet=SampleSheet, # filename="IGVExample.html", # basedirectory=getwd(), # genome="mm9") ## ----maketracktable_WithColoursAndScales, eval=FALSE-------------------------- # # igvDisplayParams <- igvParam(bigwig.autoScale = "false", # bigwig.minimum = 1, # bigwig.maximum = 5) # # # HTMLreport <- maketracktable(FileSheet,SampleSheet,"IGVex2.html",getwd(),"mm9", # colourBy="Antibody", # igvParam=igvDisplayParams) ## ----sessionInfo, results='asis', eval=TRUE----------------------------------- toLatex(sessionInfo())