hap.transmit: Build parental haplotypes in nuclear families

Description

This version only computes parental haplotypes in so far as they can be derived with complete certainty. Any locus with is uncertain in the final haplotype is coded as zero.

Usage

hap.transmit(pedfile, markers=1:((ncol(pedfile) - 6)/2),
             multiple.cases=0, use.affected=TRUE)

Value

A dataframe with one row for each affected offspring. The first four columns identify the offspring by pedigree id, member id, and parental id's. The next block of columns hold the transmitted paternal haplotype. Following blocks contain the untransmitted paternal haplotype and maternal transmitted and untransmitted haplotypes.

Arguments

pedfile: The input dataframe. The first six columns contain the pedigree id, the member id, the two parental id's, the sex, and the affectation status. Subsequent fields are in pairs and represent alleles at marker loci. All variables must take integer values, with zero being taken as "missing".
markers: Integer array indicating markers to be used and their order.
multiple.cases: The action to be taken if multiple affected offspring in any pedigree. Options are (0) include all, (1) include all, but whole family is duplicated and only one offspring is treated as affected in each repeated family, and (2) use only first affected offspring.
use.affected: If TRUE, data from affected offspring is used when imputing any missing parental data. Otherwise it is ignored.

References

Clayton, D. and Jones, H. (1999) Transmission/disequilibrium tests for extended marker haplotypes. Am. J. Hum. Gen., 65:1161-1169.

Examples

Run this code

if (FALSE) {
# Read a pedfile (which includes the variable names in the top line) 
# and build haplotypes using the markers which appear third, second, and 
# first in the pedfile. 

  filespec <- system.file("tests/test.ped", package="tdthap")
  ped <- read.table(filespec)

  haps <- hap.transmit(ped, markers=c(3,2,1))

}