RFGLS (version 1.0)

resVCmtx: Residual variance-covariance matrix.

Description

The residual covariance matrix used in package examples.

Usage

data(resVCmtx)

format

An object of class bdsmatrix (from package bdsmatrix). It is a 4050-by-4050 block-diagonal sparse matrix, with off-diagonal elements of 0. It has six slots, the descriptions of which may be found in the documentation for bdsmatrix-class.

Details

It is perhaps most instructive to see the syntax by which resVCmatrix can be reproduced from datasets pheno, geno, and pedigree: data(pheno) data(geno) data(pedigree) foo <- gls.batch.get( phenfile=pheno, genfile=data.frame(t(geno)), pedifile=pedigree, outfile="example_output.txt", covmtxfile.in=NULL,covmtxfile.out=paste(phen,"_cov_matrix.txt",sep=""), phen="Zscore", covars = "IsFemale", med = "rfgls", sizeLab = "OOPP", Mz = TRUE, Bo = TRUE, Ad = TRUE, Mix = TRUE, indobs = TRUE, col.names = TRUE, pediheader = FALSE, pedicolname=c("FAMID","ID","PID","MID","SEX"), sep.phe = " ", sep.gen = " ", sep.ped = " ") bar <- fgls( fixed=Zscore ~ IsFemale, data=foo$test.dat, sizelist=foo$sizelist, tlist=foo$tlist, sizeLab="OOPP",Mz = TRUE, Bo = TRUE, Ad = TRUE, Mix = TRUE, indobs = TRUE, get.hessian=FALSE,vmat = NULL, subset=NULL, weights=NULL, na.action=NULL) Then, bar$sigma is identical to resVCmtx.

Examples

data(resVCmtx)
str(resVCmtx)
##Also see examples for functions fgls() and gls.batch().