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

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Documentation for package ‘CODEX’ version 1.34.0

• 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