derfinder (version 1.6.4)

getRegionCoverage: Extract coverage information for a set of regions

Description

This function extracts the raw coverage information calculated by fullCoverage at each base for a set of regions found with calculatePvalues. It can further calculate the mean coverage per sample for each region.

Usage

getRegionCoverage(fullCov = NULL, regions, totalMapped = NULL,
  targetSize = 8e+07, files = NULL, ...)

Arguments

fullCov

A list where each element is the result from loadCoverage used with returnCoverage = TRUE. Can be generated using fullCoverage. Alternatively, specify files to extract the coverage information from the regions of interest. This can be helpful if you do not wish to store fullCov for memory reasons.

regions

The $regions output from calculatePvalues. It is important that the seqlengths information is provided.

totalMapped

The total number of reads mapped for each sample. Providing this data adjusts the coverage to reads in targetSize library. By default, to reads per 80 million reads.

targetSize

The target library size to adjust the coverage to. Used only when totalMapped is specified.

files

A character vector with the full path to the sample BAM files (or BigWig files). The names are used for the column names of the DataFrame. Check rawFiles for constructing files. files can also be a BamFileList object created with BamFileList or a BigWigFileList object created with BigWigFileList.

...

Arguments passed to other methods and/or advanced arguments.

Value

• a list of data.frame where each data.frame has the coverage information (nrow = width of region, ncol = number of samples) for a given region. The names of the list correspond to the region indexes in regions

Details

When fullCov is the output of loadCoverage with cutoff non-NULL, getRegionCoverage assumes that the regions come from the same data. Meaning that filterData was not used again. This ensures that the regions are a subset of the data available in fullCov.

If fullCov is NULL and files is specified, this function will attempt to read the coverage from the files. Note that if you used 'totalMapped' and 'targetSize' before, you will have to specify them again to get the same results.

See also advancedArg with fun='loadCoverage' for other details.

You should use at most one core per chromosome.

See Also

fullCoverage, calculatePvalues

Examples

## Obtain fullCov object
fullCov <- list('21'=genomeDataRaw$coverage)

## Assign chr lengths using hg19 information, use only first two regions
library('GenomicRanges')
data(hg19Ideogram, package = 'biovizBase', envir = environment())
regions <- genomeRegions$regions[1:2]
seqlengths(regions) <- seqlengths(hg19Ideogram)[names(seqlengths(regions))]

## Finally, get the region coverage
regionCov <- getRegionCoverage(fullCov=fullCov, regions=regions)