R/pedigree.shrink.minor.R

In sinnweja/kinship2: Pedigree Functions

# Automatically generated from all.nw using noweb
# TODO add documentation
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)
}