Normalization of read depth from whole exome sequencing
Description
Fits a Poisson loglinear 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
1  normalize(Y_qc, gc_qc, K)

Arguments
Y_qc 
Read depth matrix after quality control procedure returned from

gc_qc 
Vector of GC content for each exon after quality control procedure returned
from 
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
1 2 3 4 5 6 7 8 