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

In lcolladotor/derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

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

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.

Author(s)

Leonardo Collado-Torres

See Also

fullCoverage, sampleDepth

Examples

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

## End(Not run)

lcolladotor/derfinder documentation built on Dec. 17, 2024, 4:53 p.m.