qc {CODEX} | R Documentation |
Applies a quality control procedure to the depth of coverage matrix both sample-wise and exon-wise before normalization.
qc(Y, sampname, chr, ref, mapp, gc,cov_thresh,length_thresh,mapp_thresh, gc_thresh)
Y |
Original read depth matrix returned from |
sampname |
Vector of sample names returned from |
chr |
Chromosome. |
ref |
IRanges object specifying exonic positions returned from
|
mapp |
Vector of mappability for each exon returned from |
gc |
Vector of GC content for each exon returned from |
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. |
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.
Y_qc |
Updated |
sampname_qc |
Updated |
gc_qc |
Updated |
mapp_qc |
Updated |
ref_qc |
Updated |
qcmat |
Matrix specifying results of exon-wise QC procedures |
Yuchao Jiang yuchaoj@wharton.upenn.edu
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