normalize {CODEX} | R Documentation

## Normalization of read depth from whole exome sequencing

### Description

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.

### Usage

    normalize(Y_qc, gc_qc, K)

### Arguments

`Y_qc` | Read depth matrix after quality control procedure returned from `qc`
`gc_qc` | Vector of GC content for each exon after quality control procedure returned from `qc`
`K` | Number of latent Poisson factors. Can be an integer if optimal solution has been chosen or a vector of integers so that AIC, BIC, and RSS are computed for choice of optimal k.

### Value

`Yhat` | Normalized read depth matrix
`AIC` | AIC for model selection
`BIC` | BIC for model selection
`RSS` | RSS for model selection
`K` | Number of latent Poisson factors

### Author(s)

Yuchao Jiang yuchaoj@wharton.upenn.edu

### See Also

`qc`, `choiceofK`

### Examples

    Y_qc <- qcObjDemo$Y_qc
    gc_qc <- qcObjDemo$gc_qc
    normObj <- normalize(Y_qc, gc_qc, K = 1:5)
    Yhat <- normObj$Yhat
    AIC <- normObj$AIC
    BIC <- normObj$BIC
    RSS <- normObj$RSS
    K <- normObj$K

[Package CODEX version 1.12.0 Index]