getmapp: Get mappability for each exonic target

In CODEX: A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

Description

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

Usage

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 [e-mail]

See Also

getbambed, qc

Examples

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

CODEX documentation built on Nov. 8, 2020, 8:22 p.m.