# A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

## Documentation for package ‘CODEX’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

CODEX-package | A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
bambedObjDemo | Demo data pre-stored for bambedObj.
choiceofK | Determine the number of latent factors K.
CODEX | A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
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 the case-control setting
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 genotyping