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Last data update: 2014.03.03

R: Quality control procedure for depth of coverage

qc	R Documentation

Quality control procedure for depth of coverage

Description

Applies a quality control procedure to the depth of coverage matrix both sample-wise and exon-wise before normalization.

Usage

qc(Y, sampname, chr, ref, mapp, gc,cov_thresh,length_thresh,mapp_thresh,
  gc_thresh)

Arguments

`Y`	Original read depth matrix returned from `getcoverage`
`sampname`	Vector of sample names returned from `getbambed`
`chr`	Chromosome.
`ref`	IRanges object specifying exonic positions returned from `getbambed`
`mapp`	Vector of mappability for each exon returned from `getmapp`
`gc`	Vector of GC content for each exon returned from `getgc`
`cov_thresh`	Vector specifying the upper and lower bound of exonic median coverage threshold for QC. 20-4000 recommended.
`length_thresh`	Vector specifying the upper and lower bound of exonic length threshold for QC. 20-2000 recommended.
`mapp_thresh`	Scalar variable specifying exonic mappability threshold for QC. 0.9 recommended.
`gc_thresh`	Vector specifying the upper and lower bound of exonic GC content threshold for QC. 20-80 recommended.

Details

It is suggested that analysis by CODEX be carried out in a batch-wise fashion if multiple batches exist. CODEX further filters out exons that: have extremely low coverage–median read depth across all samples less than 20 or greater than 4000; are extremely short–less than 20 bp; are extremely hard to map– mappability less than 0.9; have extreme GC content–less than 20 or greater than 80. The above filtering thresholds are recommended and can be user-defined to be adapted to different sequencing protocols.

Value

`Y_qc`	Updated `Y` after QC
`sampname_qc`	Updated `sampname` after QC
`gc_qc`	Updated `gc` after QC
`mapp_qc`	Updated `mapp` after QC
`ref_qc`	Updated `ref` after QC
`qcmat`	Matrix specifying results of exon-wise QC procedures

Author(s)

Yuchao Jiang yuchaoj@wharton.upenn.edu

Examples

Y <- coverageObjDemo$Y
sampname <- bambedObjDemo$sampname
chr <- bambedObjDemo$chr
ref <- bambedObjDemo$ref
gc <- gcDemo
mapp <- mappDemo
cov_thresh <- c(20, 4000)
length_thresh <- c(20, 2000)
mapp_thresh <- 0.9
gc_thresh <- c(20, 80)
qcObj <- qc(Y, sampname, chr, ref, mapp, gc, cov_thresh, length_thresh, 
    mapp_thresh, gc_thresh)
Y_qc <- qcObj$Y_qc
sampname_qc <- qcObj$sampname_qc
gc_qc <- qcObj$gc_qc
mapp_qc <- qcObj$mapp_qc
ref_qc <- qcObj$ref_qc
qcmat <- qcObj$qcmat

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/qc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: qc
> ### Title: Quality control procedure for depth of coverage
> ### Aliases: qc
> ### Keywords: package
> 
> ### ** Examples
> 
> Y <- coverageObjDemo$Y
> sampname <- bambedObjDemo$sampname
> chr <- bambedObjDemo$chr
> ref <- bambedObjDemo$ref
> gc <- gcDemo
> mapp <- mappDemo
> cov_thresh <- c(20, 4000)
> length_thresh <- c(20, 2000)
> mapp_thresh <- 0.9
> gc_thresh <- c(20, 80)
> qcObj <- qc(Y, sampname, chr, ref, mapp, gc, cov_thresh, length_thresh, 
+     mapp_thresh, gc_thresh)
Excluded 21 exons due to extreme coverage.
Excluded 0 exons due to extreme exonic length.
Excluded 3 exons due to extreme mappability.
Excluded 0 exons due to extreme GC content.
After taking union, excluded 23 out of 100 exons in QC.
> Y_qc <- qcObj$Y_qc
> sampname_qc <- qcObj$sampname_qc
> gc_qc <- qcObj$gc_qc
> mapp_qc <- qcObj$mapp_qc
> ref_qc <- qcObj$ref_qc
> qcmat <- qcObj$qcmat
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>