Get mappability for each exonic target

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Description

Computes mappability for each exon. To save running time, take values from pre-computed results. Will be later used in QC procedure.

Usage

1
getmapp(chr, ref)

Arguments

chr

Chromosome returned from getbambed

ref

IRanges object returned from getbambed

Details

To calculate the exonic mappability, we first construct consecutive reads of length 90 that are one base pair apart along the exon. The sequences are taken from the hg19 reference. We then find possible positions across the genome that the reads can map to allowing for two mismatches. We compute the mean of the probabilities that the overlapped reads map to the target places where they are generated and use this as the mappability of the exon.

Value

Vector of mappability for each exon.

Author(s)

Yuchao Jiang yuchaoj@wharton.upenn.edu

See Also

getbambed, qc

Examples

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ref <- IRanges(st = 51207851, end = 51207982)
mapp <- getmapp(chr = 22, ref)