MakeIGVSampleMetadata {tracktables} | R Documentation |
Creates sample metadata file for IGV from a Samplesheet of metadata and FileSheet of file locations.
MakeIGVSampleMetadata(SampleSheet, fileSheet, igvdirectory)
SampleSheet |
A data.frame object with metadata information for samples. First column must contain unique sample ids. |
fileSheet |
A data.frame of file locations. First column must contain the unique sample ids. |
igvdirectory |
A character of the directory to which sample metadata file is written. |
A character of file location for the IGV sample information file.
Thomas Carroll
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") MakeIGVSampleMetadata(SampleSheet,fileSheet,igvdirectory=getwd())