derfinder (version 1.6.4)

collapseFullCoverage: Collapse full coverage information for efficient quantile computations

Description

For a given data set this function collapses the full coverage information for each sample from all the chromosomes. The resulting information per sample is the number of bases with coverage 0, 1, etc. It is similar to using table() on a regular vector. This information is then used by sampleDepth for calculating the sample depth adjustments. The data set can loaded to R using (see fullCoverage) and optionally filtered using filterData.

Usage

collapseFullCoverage(fullCov, colsubset = NULL, save = FALSE, ...)

Arguments

fullCov

A list where each element is the result from loadCoverage used with cutoff=NULL. Can be generated using fullCoverage.

colsubset

Which columns of coverageInfo$coverage to use.

save

If TRUE, the result is saved as 'collapsedFull.Rdata'.

...

Arguments passed to other methods and/or advanced arguments.

Value

• A list with one element per sample. Then per sample, a list with two vector elements: values and weights. The first one is the coverage value and the second one is the number of bases with that value.

See Also

fullCoverage, sampleDepth

Examples

## Collapse the coverage information for the filtered data
collapsedFull <- collapseFullCoverage(list(genomeData), 
    verbose=TRUE)
collapsedFull

## You can also collapsed the raw data
collapsedFullRaw <- collapseFullCoverage(list(genomeDataRaw), verbose=TRUE)