A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.
|Author||Yuchao Jiang, Nancy R. Zhang|
|Date of publication||None|
|Maintainer||Yuchao Jiang <email@example.com>|
bambedObjDemo: Demo data pre-stored for bambedObj.
choiceofK: Determine the number of latent factors K.
CODEX-package: A Normalization and Copy Number Variation Detection Method...
coverageObjDemo: Demo data pre-stored for coverageObj.
gcDemo: Demo data pre-stored for GC content.
getbambed: Get bam file directories, sample names, and exonic positions
getcoverage: Get depth of coverage from whole exome sequencing
getgc: Get GC content for each exonic target
getmapp: Get mappability for each exonic target
mappability: Pre-computed mappabilities
mappDemo: Demo data pre-stored for mappability.
mapp_ref: Position reference for pre-computed mappability results.
normalize: Normalization of read depth from whole exome sequencing
normalize2: Normalization of read depth from whole exome sequencing under...
normObjDemo: Demo data pre-stored for normObj.
qc: Quality control procedure for depth of coverage
qcObjDemo: Demo data pre-stored for qcObj.
segment: Recursive segmentation algorithm for CNV detection and...