collapseFullCoverage: Collapse full coverage information for efficient quantile...

View source: R/collapseFullCoverage.R

collapseFullCoverageR Documentation

Collapse full coverage information for efficient quantile computations


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.


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



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


Which columns of coverageInfo$coverage to use.


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


Arguments passed to other methods and/or advanced arguments. Advanced arguments:


If TRUE basic status updates will be printed along the way. Default: FALSE.


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.


Leonardo Collado-Torres

See Also

fullCoverage, sampleDepth


## Collapse the coverage information for the filtered data
collapsedFull <- collapseFullCoverage(list(genomeData),
    verbose = TRUE
## Not run: 
## You can also collapsed the raw data
collapsedFullRaw <- collapseFullCoverage(list(genomeDataRaw), verbose = TRUE)

## End(Not run)

lcolladotor/derfinder documentation built on May 4, 2024, 5:38 p.m.