calcBins {MDTS} | R Documentation |
This function will randomly select a sample of bam files to calculate dynamic MDTS bins for subsequent read-depth analysis.
calcBins(metaData, n, readLength, medianCoverage, minimumCoverage, genome, mappabilityFile, seed = 1337)
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. |
Returns a GRanges
object depicting the dynamic bins that MDTS
calculates.
load(system.file("extdata", 'bins.RData', package = "MDTS")) bins