multiTEQCreport: Creates an html report for multiple samples
In TEQC: Quality control for target capture experiments

Description Usage Arguments Details Value Author(s) References See Also Examples

Creates an automated html report comparing TEQC analysis results of several samples

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multiTEQCreport(singleReportDirs, samplenames, projectName = "", targetsName = "",
          referenceName = "", destDir = "multiTEQCreport", k = c(1, 2, 3, 5, 10, 20), figureFormat = c("jpeg", "png", "tiff"))

`singleReportDirs`	string of directory names; output directories of function TEQCreport(), launched beforehand for each single sample
`samplenames`	names of the samples that will be used in tables and figures
`projectName`	descriptive name for the project / collection of samples; will be written on top of the html report
`targetsName`	descriptive name of the captured target; will be written on top of the html report
`referenceName`	descriptive name of the reference genome the reads were aligned against; will be written on top of the html report
`destDir`	directory where results and html documents shall be saved
`k`	integer vector of `k`-values for which to show fraction of target bases with coverage >= `k` in section 'Sensitivity'
`figureFormat`	format of the figures produced for the html report (besides pdf graphs)

Before creating the html report for multiple samples, TEQCreport has to be run for each of the samples separately. The output directories of those analyses are the input for multiTEQCreport. While the creation of single-sample reports is time and memory intensive, multiTEQCreport finishes quickly, since it just collects and summarizes the results from the single analyses. The files for the multiple sample html report are created in destDir. The report can be viewed by opening destDir/index.html in a web browser. Images are saved in destDir/image.

The function is invoked for its side effect

Manuela Hummel m.hummel@dkfz.de

Hummel M, Bonnin S, Lowy E, Roma G. TEQC: an R-package for quality control in target capture experiments. Bioinformatics 2011; 27(9):1316-7.

TEQCreport

## get reads and targets
exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, skip=0, idcol=4)
targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
targets <- get.targets(targetsfile, skip=0) 

## simulated 2nd sample
r <- sample(length(reads), 0.1 * length(reads))
reads2 <- reads[-r,,drop=TRUE]

## Not run: 
## create single-sample reports
TEQCreport(sampleName="Test Sample A", targetsName="Human Exome", referenceName="Human Genome",
          destDir="./reportA", reads=reads, targets=targets, genome="hg19")
TEQCreport(sampleName="Test Sample B", targetsName="Human Exome", referenceName="Human Genome",
          destDir="./reportB", reads=reads2, targets=targets, genome="hg19")
          
## create multi-sample report
multiTEQCreport(singleReportDirs=c("./reportA", "./reportB"), samplenames=c("Sample A","Sample B"), 
          projectName="Test Project", targetsName="Human Exome", referenceName="Human Genome", 
          destDir="./multiTEQCreport")
          
## End(Not run)