extraBinomial-package:
Extra-binomial approach for pooled sequencing data
Description
This package tests for differences in minor allele frequency between
groups and is based on extra-binomial variation model for pooled sequencing data.
Details
|
Package: |
| extraBinomial |
|
Type: |
| Package |
|
Version: |
| 2.1 |
|
Date: |
| 2012-07-09 |
|
License: |
| GPL-3 |
To use the function exbio, simply define two matrices R, R.alt with the
same dimensions (rows index SNPs and columns index pools), a vector cc
indicating the case and control status, number of chromosomes (n) and
then do: exbio(R, R.alt, cc, n) to yield the estimated allele frequencies and p-value based on extra-binomial model.
References
Yang et al. "Extra-binomial variation approach for analysis of pooled DNA sequencing data", under review.