multiTEQCreport: Creates an html report for multiple samples

In hummelma/TEQC: Quality control for target capture experiments

Description

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

Usage

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

Arguments

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)

Details

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.

Value

The function is invoked for its side effect

Author(s)

Manuela Hummel [e-mail]

References

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.

See Also

TEQCreport

Examples

## 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)

hummelma/TEQC documentation built on March 22, 2021, 9:45 a.m.