tracktables (version 1.6.2)

maketracktable: Make HTML pages for IGV sessions (Tracktables Experiment Report)

Description

Creates HTML table of sample metadata and all required files for interacting with IGV.

Usage

maketracktable(fileSheet, SampleSheet, filename, basedirectory, genome,
  colourBy = NULL, igvParams = igvParam())

Arguments

fileSheet

A data frame containing sample file locations (e.g. BigWig locations).

SampleSheet

A data frame containing sample metadata

filename

Character of name for tracktables HTML report. (.html prefix is added automatically)

basedirectory

Character of directory for tracktables HTML report, IGV sessions and any interval files

genome

Character of genome for IGV (See IGV user guide for details)

colourBy

Character defining which sample metadata to be used for colouring bigwig files

igvParams

An object of class igvParam containing display parameters for IGV. When providing a list, this list must be same length as number of samples and each element have two numeric values corresponding to minimum and maximum value to be used in setting data range. Currently only "autoscale" or a list of minimum and maximum values are accepted.

Value

• An object containing XML document (HTMLInternalDocument,XMLInternalDocument,XMLAbstractDocument)

Examples

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")
  HTMLreport <- maketracktable(fileSheet,SampleSheet,
                               "IGV_Example.html",
                               basedirectory=getwd(),
                               "mm9")