coverageToExon: Extract coverage information for exons

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

Extract coverage information for exons

Description

This function extracts the coverage information calculated by fullCoverage for a set of exons determined by makeGenomicState. The underlying code is similar to getRegionCoverage with additional tweaks for calculating RPKM values.

Usage

coverageToExon(
  fullCov = NULL,
  genomicState,
  L = NULL,
  returnType = "raw",
  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.
genomicState	A GRanges object created with makeGenomicState. It can be either the genomicState$fullGenome or genomicState$codingGenome component.
L	The width of the reads used. Either a vector of length 1 or length equal to the number of samples.
returnType	If raw, then the raw coverage information per exon is returned. If rpkm, RPKM values are calculated for each exon.
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. Advanced arguments: verbose If TRUE basic status updates will be printed along the way. BPPARAM.strandStep A BPPARAM object to use for the strand step. If not specified, then strandCores specifies the number of cores to use for the strand step. The actual number of cores used is the minimum of strandCores, mc.cores and the number of strands in the data. BPPARAM.chrStep A BPPRAM object to use for the chr step. If not specified, then mc.cores specifies the number of cores to use for the chr step. The actual number of cores used is the minimum of mc.cores and the number of samples. Passed to extendedMapSeqlevels and define_cluster.

Details

Parallelization is used twice. First, it is used by strand. Second, for processing the exons by chromosome. So there is no gain in using mc.cores greater than the maximum of the number of strands and number of chromosomes.

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.

Value

A matrix (nrow = number of exons in genomicState corresponding to the chromosomes in fullCov, ncol = number of samples) with the number of reads (or RPKM) per exon. The row names correspond to the row indexes of genomicState$fullGenome (if fullOrCoding='full') or genomicState$codingGenome (if fullOrCoding='coding').

Author(s)

Andrew Jaffe, Leonardo Collado-Torres

See Also

fullCoverage, getRegionCoverage

Examples

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

## Use only the first two exons
smallGenomicState <- genomicState
smallGenomicState$fullGenome <- smallGenomicState$fullGenome[
    which(smallGenomicState$fullGenome$theRegion == "exon")[1:2]
]

## Finally, get the coverage information for each exon
exonCov <- coverageToExon(
    fullCov = fullCov,
    genomicState = smallGenomicState$fullGenome, L = 36
)

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