pedigree: Pedigree table

In RFGLS: Rapid Feasible Generalized Least Squares

Description

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

Usage

data(pedigree)

Format

A data frame with 4050 observations on the following 6 integer-valued variables:

FAMID

"Family ID." Each family in the dataset is uniquely identified by a value of FAMID, which are all multiples of 10.

ID

Individual ID. Each subject in the dataset is uniquely identified by a value of ID.

PID

"Paternal ID." Coded 0 for founders (parents, adoptees, and "independent observations.")

MID

"Maternal ID." Coded 0 for founders (parents, adoptees, and "independent observations.")

SEX

Coded 1 for male and 2 for female.

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 strictly require is ID; see examples below.

Examples

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

foo <- gls.batch.get(
  phenfile=pheno,genfile=data.frame(t(geno)),pedifile=pedigree,
  covmtxfile.in=NULL,theta=NULL,snp.names=map[,2],
  input.mode=1,
  pediheader=FALSE,pedicolname=c("FAMID","ID","PID","MID","SEX"),
  sep.phe=" ",sep.gen=" ",sep.ped=" ",
  phen="Zscore",covars="IsFemale",med=c("UN","VC"),
  outfile,col.names=TRUE,return.value=FALSE,
  covmtxfile.out=NULL,
  covmtxparams.out=NULL,
  sizeLab=NULL,Mz=NULL,Bo=NULL,Ad=NULL,Mix=NULL,indobs=NULL)
str(foo)

##Also works, since phenfile provides 'FTYPE' and 'INDIV',
##and input.mode=1:
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.
  covmtxfile.in=NULL,theta=NULL,snp.names=map[,2],
  input.mode=1, ##<-- =2 or =3 would need more pedifile columns
  pediheader=FALSE,pedicolname=c("FAMID","ID","PID","MID","SEX"),
  sep.phe=" ",sep.gen=" ",sep.ped=" ",
  phen="Zscore",covars="IsFemale",med=c("UN","VC"),
  outfile,col.names=TRUE,return.value=FALSE,
  covmtxfile.out=NULL,
  covmtxparams.out=NULL,
  sizeLab=NULL,Mz=NULL,Bo=NULL,Ad=NULL,Mix=NULL,indobs=NULL)
str(foo2)

RFGLS documentation built on May 2, 2019, 2:51 p.m.