TEQCreport: Creates an html report
In TEQC: Quality control for target capture experiments

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

Creates an automated html report for the complete TEQC analysis of one sample

TEQCreport(sampleName = "", targetsName = "", referenceName = "", destDir = "TEQCreport",
            reads = get.reads(), targets = get.targets(), Offset = 0, pairedend = FALSE, genome = c(NA, "hg38", "hg19", "hg18"),
            genomesize, k=c(1, 2, 3, 5, 10, 20), covthreshold = 8, CovUniformityPlot = FALSE, CovTargetLengthPlot = FALSE, CovGCPlot = FALSE,
            duplicatesPlot = FALSE, baits = get.baits(), WigFiles = FALSE, saveWorkspace = FALSE, figureFormat = c("jpeg", "png", "tiff"))

`sampleName`	descriptive sample name; 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
`reads`	`RangedData` table containing positions of sequenced reads, or call to `get.reads` to read in positions from a bed or BAM file
`targets`	`RangedData` table containing positions of target regions, or call to `get.targets` to read in positions from a bed file
`Offset`	integer; add `Offset` bases on both sides to targeted regions and potentially collapse resulting overlapping target regions
`pairedend`	if `TRUE`, data will be considered to be paired-end data, i.e. reads will be "merged" to read pairs, and chromosome bar plot, specificity, enrichment and duplicate analysis (if selected) will be based on read pairs rather than on single reads
`genome`	genome version targets were designed and reads aligned to. For the given options the total genome size is set automatically. For other genomes or versions, leave this option empty ('NA') and specify the genome size with option 'genomesize'
`genomesize`	integer: specify the total genome size manually. If 'genomesize' is given, option 'genome' will be ignored.
`k`	integer vector of `k`-values for which to show fraction of target bases with coverage >= `k` in 'Sensitivity' table. Passed to `covered.k`
`covthreshold`	integer indicating which coverage value shall be highlighted by dashed lines in the coverage histogram. Passed to `coverage.hist`
`CovUniformityPlot`	if `TRUE`, a coverage uniformity plot is created, see `coverage.uniformity`
`CovTargetLengthPlot`	if `TRUE`, coverage vs target length plots are created, see `coverage.targetlength.plot`
`CovGCPlot`	if `TRUE`, a coverage vs GC content plot is created, see `coverage.GC`
`duplicatesPlot`	if `TRUE`, a duplicates barplot is created, see `duplicates.barplot`
`baits`	A `RangedData` table holding the hybridization probe ("bait") positions and sequences, or call to `get.baits` to read in positions from a bed file. Only needed if `CovGCPlot = TRUE`.
`WigFiles`	if `TRUE`, wiggle files with per-base coverage are created for each chromosome
`saveWorkspace`	if `TRUE`, an R workspace with objects `reads`, `targets` and output of `coverage.target` and `reads2pairs` (in case `pairedend = TRUE`) are saved in `destDir` to be available for further analyses
`figureFormat`	format of the figures produced for the html report (besides pdf graphs)

TEQC analysis is performed and files for an 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. Wiggle files (in case WigFiles = TRUE) are saved in destDir/wiggle. A table with general target coverage statistics, a table with average coverage values per target, a table with cumulative fractions of targeted bases with certain coverage and the R workspace containing R objects for potential further analysis (in case saveWorkspace = TRUE) are saved in destDir.

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):1316-1317

get.reads, get.targets, fraction.target, fraction.reads.target, coverage.target, readsPerTarget, reads2pairs, covered.k, coverage.hist, coverage.uniformity, coverage.targetlength.plot, coverage.GC, get.baits, make.wigfiles

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

## create report
## Not run: 
TEQCreport(sampleName="Test Sample", targetsName="Human Exome", referenceName="Human Genome",
          destDir="report", reads=get.reads(readsfile, skip=0, idcol=4),
          targets=get.targets(targetsfile, skip=0), genome="hg19")
## End(Not run)

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: hwriter
[1] "results and report are saved in folder /work/tmp/report"
[1] "reading data..."
[1] "read 19546 sequenced reads"
[1] "read 50 (non-overlapping) target regions"
[1] "calculating fraction of on-target reads"
[1] "calculating coverage..."
[1] "counting reads per target..."
[1] "generating figures..."
[1] "generating html report..."
Warning message:
system call failed: Cannot allocate memory