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


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Documentation for package ‘CODEX’ version 1.26.0

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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