qc {CODEX} | 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

### See Also

`getbambed`, `getgc`, `getmapp`

### 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

[Package CODEX version 1.16.0 Index]