Calculate the total number of mapped reads

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Description

For a given BAM calculate the total number of mapped reads and for a BigWig file calculate the area under the curve (AUC), which is related to the number of mapped reads: the exact relationship depends on whether the aligner soft clips reads and/or if the length of the reads is the same. If you use the 'chrs' argument you can choose to only consider the information for your chromosomes of interest. For example, you can exclude the mitocondrial chromosome.

Usage

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getTotalMapped(rawFile, chrs = NULL)

Arguments

rawFile

Either a BAM file or a BigWig file.

chrs

If NULL, all the chromosomes will be used. Otherwise, only those in chrs will be used.

Value

The total number of mapped reads for a BAM file or the AUC for a BigWig file in a single element vector.

Author(s)

Leonardo Collado-Torres

Examples

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## Get the total number of mapped reads for an example BAM file:
bam <- system.file('extdata', 'genomeData', 'ERR009102_accepted_hits.bam',
    package='derfinder', mustWork=TRUE)
getTotalMapped(bam)

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