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Recursive segmentation algorithm for CNV detection and genotyping, using normalized read depth from whole exome sequencing.
● Data Source:
BioConductor
● Keywords: package
● Alias: segment
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CODEX is 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.
● Data Source:
BioConductor
● Keywords: package
● Alias: CODEX, CODEX-package
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Determines the number of latent variables K via AIC, BIC, and deviance reduction. A pdf file containing all three plots is generated.
● Data Source:
BioConductor
● Keywords: package
● Alias: choiceofK
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Gets bam file directories, sample names from .txt file, and exonic positions from .bed file.
● Data Source:
BioConductor
● Keywords: package
● Alias: getbambed
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Gets depth of coverage for each exon across all samples from whole exome sequencing files.
● Data Source:
BioConductor
● Keywords: package
● Alias: getcoverage
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Computes GC content for each exon. Will be later used in QC procedure and normalization.
● Data Source:
BioConductor
● Keywords: package
● Alias: getgc
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Computes mappability for each exon. To save running time, take values from pre-computed results. Will be later used in QC procedure.
● Data Source:
BioConductor
● Keywords: package
● Alias: getmapp
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Fits a Poisson log-linear model that normalizes the read depth data from whole exome sequencing. Includes terms that specifically remove biases due to GC content, exon capture and amplification efficiency, and latent systemic artifacts.
● Data Source:
BioConductor
● Keywords: package
● Alias: normalize
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Fits a Poisson log-linear model that normalizes the read depth data from whole exome sequencing. Includes terms that specifically remove biases due to GC content, exon capture and amplification efficiency, and latent systemic artifacts. If the WES is designed under case-control setting, CODEX estimates the exon-wise Poisson latent factor using only the read depths in the control cohort, and then computes the sample-wise latent factor terms for the case samples by regression.
● Data Source:
BioConductor
● Keywords: package
● Alias: normalize2
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Applies a quality control procedure to the depth of coverage matrix both sample-wise and exon-wise before normalization.
● Data Source:
BioConductor
● Keywords: package
● Alias: qc
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providing 
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