RFGLS (version 1.0)

pedigree: Pedigree table

Description

A pedigree table for the same simulees as in dataset pheno.

Usage

data(pedigree)

Details

Merely a pedigree table in a commonly used format. Note that its column names are the default names that gls.batch() or gls.batch.get() assign to the pedigree file. However, the only column that those two functions require is ID; see examples below.

Examples

data(pedigree)
data(pheno)
data(geno)

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 = "")
str(foo)

##Also works:
pedigree2 <- pedigree
pedigree2[,-2] <- NA    ##<--Change all but column 'ID' to NA.
foo2 <- gls.batch.get(
  phenfile=pheno,
  genfile=data.frame(t(geno)),
  pedifile=pedigree2,             ##<--Note change.
  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 = "")