maketracktable: Make HTML pages for IGV sessions (Tracktables Experiment...

In tracktables: Build IGV tracks and HTML reports

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)

Author(s)

Thomas Carroll

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")

Example output

tracktables uses the Datatables javascript libraries.
            For information on Datatables see http://datatables.net/
[1] "169,169,169"
[1] "169,169,169"
[1] "169,169,169"
[1] "169,169,169"

tracktables documentation built on Nov. 8, 2020, 5:28 p.m.