calcBins: Sample driven calculation of bins for counting

Description Usage Arguments Value Examples

View source: R/calcBins.R

Description

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

Usage

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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

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

MDTS documentation built on Nov. 1, 2018, 2:24 a.m.