calcBins: Sample driven calculation of bins for counting

In JMF47/DnMD: Detection of de novo deletion in targeted sequencing trios

Description

This function will randomly select a sample of bam files to calculate dynamic MDTS bins for subsequent read-depth analysis.

Usage

calcBins(metaData, n, readLength, medianCoverage, minimumCoverage, genome,
  mappabilityFile, seed = 1337)

Arguments

metaData	A table in the format of the output of getMetaData().
n	The number of subsamples to use.
readLength	The read length of the experiment.
medianCoverage	The median number of reads across sub-samples to reach before creating a new bin.
minimumCoverage	The miminum number of coverage across all sub-samples required to create the proto-region.
genome	The BSGenome object that assists in calculations of the GC content of the bins.
mappabilityFile	A path to the bigwig file of 100mer mappability of the corresponding genome.
seed	Sets the seed so results are reproducible. Defaults to 1337.

Value

Returns a GRanges object depicting the dynamic bins that MDTS calculates.

Examples

load(system.file("extdata", 'bins.RData', package = "MDTS"))
bins

JMF47/DnMD documentation built on May 31, 2019, 10:44 p.m.