determineQuantiles: Determines basewise user-defined quantiles

In BadRegionFinder: BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

Description

The function determineQuantiles provides a possibility to determine user-definable quantiles for every base previously analyzed. Thereby, the quantiles are determined over all samples.

Usage

determineQuantiles(coverage_summary, quantiles, output)

Arguments

coverage_summary	List object, return value of function determineCoverage.
quantiles	Vector determining the quantiles to be calculated.
output	The folder to write the output files into.

Details

The function determineQuantiles serves to determine a set of user-defined quantiles at each position over all samples. Every single base is analyzed, except for the case when the bases were not originally targeted and if no coverage is detected by any of the samples. In this case the corresponding region is summed up.

Files get written out in the form: "Quantiles_chr<chromosomename>.txt".

Value

A list is returned. Every component contains the coverage information of one chromosome as a GRanges object. The metadata columns contain information on the coverage according to the previously defined quantiles. Furthermore, the column 'TargetBases' contains information on whether the considered region or position contains target bases (value 1) or not (value 0).

If a chromosome has not been targeted and/or not covered by any sample, but defined in regionsOfInterest, the component is "NA".

Author(s)

Sarah Sandmann <[e-mail]>

See Also

BadRegionFinder, determineCoverage, determineCoverageQuality, determineRegionsOfInterest, reportBadRegionsSummary, reportBadRegionsDetailed, reportBadRegionsGenes, plotSummary, plotDetailed, plotSummaryGenes

Examples

library("BSgenome.Hsapiens.UCSC.hg19")

sample_file <- system.file("extdata", "SampleNames.txt", 
                           package = "BadRegionFinder")
samples <- read.table(sample_file)
bam_input <- system.file("extdata", package = "BadRegionFinder")
output <- system.file("extdata", package = "BadRegionFinder")
target_regions <- system.file("extdata", "targetRegions.bed",
                              package = "BadRegionFinder")
targetRegions <- read.table(target_regions, header = FALSE,
                            stringsAsFactors = FALSE)

coverage_summary <- determineCoverage(samples, bam_input, targetRegions, output,
                                      TRonly = TRUE)
quantiles <- c(0.25, 0.5, 0.75)
coverage_summary2 <- determineQuantiles(coverage_summary, quantiles, output)

BadRegionFinder documentation built on Nov. 8, 2020, 5:24 p.m.