strataReduce: Strata Reduction

In fbati: Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families

Strata Reduction

Description

Reduces the number of strata in nuclear pedigrees for testing (for use with FBAT-I). For nuclear families with both parents, a random affected child is drawn. For nuclear families with at least one parent missing, a random affected and another random sib is used (parents ignored).

Usage

strataReduce( data, envCol, m0, m1=m0+1, maxSib=3 )

Arguments

data	data.frame of a merged pedigree/phenotype (see mergePhePed(...)).
envCol	Integer representing environment column.
m0	Integer representing column of first marker.
m1	Integer representing column of second marker.
maxSib	Maximum number of sibs to use per family to reduce the number of strata.

Examples

## Function creates a family with the specified markers and statuses
## NOTE: affection is false/true, whereas it is coded 1/2 in the ped file
createFam <- function( pa=c(0,0), pb=c(0,0),
                       ca, cb,
                       caffected=rep(TRUE,length(ca)),
                       env=1:length(ca) ) {
  ## pid, id, idfath, idmoth, sex, affection, m0a, m0b
  numC <- length(ca)
  return( data.frame( pid=rep(1,2+numC),
                      id=1:(2+numC),
                      idfath=c(0,0,rep(1,numC)),
                      idmoth=c(0,0,rep(2,numC)),
                      sex=c(2,1,rep(0,numC)),
                      affection=c(0,0,as.integer(caffected)+1),
                      m0.a=c(pa,ca), m0.b=c(pb,cb),
                      env=c(NA,NA,env) ) )
}
## Function tests/exemplifies the strataReduce(...) routine
srFam <- function( ... ) {
  data <- createFam( ... )
  data2 <- strataReduce( data=data, envCol=9, m0=7, maxSib=2 )
  cat( "Original data:\n" )
  print( data )
  cat( "Reduced stratification data:\n" )
  print( data2 )
}

## Basic sib test
srFam( ca=c(1,1,2), cb=c(1,2,2) )

## Basic trio test
srFam( ca=c(1,1,2), cb=c(1,2,2), pa=c(1,1), pb=c(2,2) )

## a fairly comprehensive test here
## The affected should always be one of the first three,
##  the unaffected could be one the first eight
for( i in 1:10 )
  srFam( ca=c(1:8,0,0), cb=c(1:8,0,0),
         pa=c(1,1),
         caffected=c(rep(TRUE,6),rep(FALSE,4)),
         env=c(1:3,rep(NA,7)) )

## Now just to make sure, a full pedigree, rather than just one family
data <- createFam( ca=1:2, cb=1:2 )
for( i in 2:10 )
  data <- rbind( data, createFam( ca=1:2, cb=1:2 ) )
  cat( "Original data (full pedigree):\n" )
  print( data )
  cat( "Reduced stratification data (full pedigree), maxSib=3\n" )
  print( strataReduce( data=data, envCol=9, m0=7 ) )

fbati documentation built on Feb. 16, 2023, 9:31 p.m.