haplo.scan.obs

Vector of trait values, must be 1 for cases and 0 for controls.

A haplo.em object containing necessary haplotype information

em.obj

width

Slide a fixed-width window over each marker locus and scan all
possible haplotypes within the window.  For all locus-subsets, 
calculate score test statistics on observed data, and save the necessary
information for calculating the test statistics in haplo.scan.sim.

Haplo Stats is a suite of S-PLUS/R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The genetic markers are assumed to be codominant (i.e., one-to-one correspondence between their genotypes and their phenotypes), and so we refer to the measurements of genetic markers as genotypes. The main functions in Haplo Stats are:  haplo.em, haplo.glm and haplo.score.

haplo.scan.obs: For observed data, slide a fixed-width window over each marker locus and scan all possible haplotypes within the window

Description

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See Also