Description Details Author(s) References
RFGLS uses a generalized least-squares method to perform single-marker association analysis, in datasets of nuclear families containing parents, twins, and/or adoptees. It is designed for families of no greater than four members. When conducting association analysis with a large number of markers, as in GWAS, RFGLS uses rapid feasible generalized least-squares, an approximation to feasible generalized least-squares (FGLS) that considerably reduces computation time with minimal bias in p-values, and with negligible loss in power.
The package includes four functions. Function gls.batch()
actually conducts GWAS using the rapid feasible generalized least-squares approximation, under which the residual variance-covariance matrix is estimated once from a regression of the phenotype onto covariates only, and is subsequently "plugged in" for use in all subsequent single-SNP analyses. Function fgls()
is called by gls.batch()
, and conducts a single FGLS regression. It can be used to simultaneously estimate fixed-effects regression coefficients and the residual covariance matrix. Function gls.batch.get()
is useful to restructure data, for use with fgls()
. Function FSV.frompedi()
creates family-structure variables based upon available information in a pedigree file. Functions gls.batch()
and gls.batch.get()
use these family-structure variables, which represent the type of family to which each participant belongs and how s/he fits into that family.
Package: | RFGLS |
Version: | 1.1 |
Date: | 2013/8/29 |
Depends: | R (>= 2.15.0), stats, bdsmatrix, Matrix |
License: | GPL (>= 2) |
Robert M. Kirkpatrick rkirkpatrick2@vcu.edu, Xiang Li lixxx554@umn.edu, and Saonli Basu saonli@umn.edu .
Maintainer: Saonli Basu <saonli@umn.edu>
Li X, Basu S, Miller MB, Iacono WG, McGue M: A Rapid Generalized Least Squares Model for a Genome-Wide Quantitative Trait Association Analysis in Families. Human Heredity 2011;71:67-82 (DOI: 10.1159/000324839)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.