Get mappability for each exonic target

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

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

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(CODEX)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: rtracklayer

Attaching package: 'CODEX'

The following object is masked from 'package:BiocGenerics':

    normalize

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/CODEX/getmapp.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getmapp
> ### Title: Get mappability for each exonic target
> ### Aliases: getmapp
> ### Keywords: package
> 
> ### ** Examples
> 
> ref <- IRanges(st = 51207851, end = 51207982)
> mapp <- getmapp(chr = 22, ref)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>