R/pedigree.shrink.minor.R

In kinship2: Pedigree Functions

# Automatically generated from all.nw using noweb

is.parent <- function(id, findex, mindex){
  # determine subjects who are parents
  # assume input of father/mother indices, not ids

father <- mother <- rep(0, length(id))
father[findex>0] <- id[findex]
mother[mindex>0] <- id[mindex]

isFather <- !is.na(match(id, unique(father[father!=0])))
isMother <- !is.na(match(id, unique(mother[mother!=0])))
isParent <- isFather |isMother
return(isParent)
}

is.founder <- function(mother, father){
check <- (father==0) & (mother==0)
return(check)
}

is.disconnected <- function(id, findex, mindex)
{
  
  # check to see if any subjects are disconnected in pedigree by checking for
  # kinship = 0 for all subjects excluding self
  father <- id[findex]
  mother <- id[mindex]  
  kinMat <- kinship(id, father, mother)
  diag(kinMat) <- 0
  disconnected <- apply(kinMat==0.0, 1, all)
  
  return(disconnected)
}