pedHardyWeinberg {fbat}R Documentation

Test Hardy-Weinberg equilibrium for each marker based on parental data

Description

Test Hardy-Weinberg equilibrium for each marker based on parental data.

Usage

pedHardyWeinberg(geneSetObj, threshold=3, founderOnly=TRUE, quiet=FALSE)

pedHardyWeinberg.default(ped, 
          columns=c("family","pid","father","mother","sex","affected"),
          threshold=3, founderOnly=TRUE, quiet=FALSE)

Arguments

geneSetObj a geneSet object.
ped pedigree data frame whose first 6 columns are family (pedigree id), pid (patient id), father (father id), mother (mother id), sex, affected (affection status). The remaining columns are pairs of marker alleles. Each row corresponds to an individual.
columns names of the first 5 (or 6) columns of ped file. It should be either equal to c("family","pid","father","mother","sex","affected") or equal to c("family","pid","father","mother","sex")
threshold a threshold to check if expected frequencies of genotypes are too small.
founderOnly indicates if using only founder info
quiet print intermediate results if quiet=FALSE.

Value

resMat A matrix records the following quantities for all markers (rows correspond to markers): nInfoInd (number of informative individuals, i.e. individuals whose genotypes contain no missing alleles for the specified marker), nGenotype (number of possible genotypes), nHET (number of heterozygous genotypes), nHOM (number of homozygous genotypes), nAllele (number of alleles), nMissing (number of missing alleles), chi2 (chi square test statistic), df (degree of freedom of the chi square test statistic under H0), p-value (pvalue of the test).
genotype A list of possible genotypes and their frequencies for all markers.
nGenotype.vec A vector of numbers of possible genotypes for all markers.
piVec Allele frequencies for all markers.

Author(s)

Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu

Examples

  data(CAMP)
  res<-pedHardyWeinberg(CAMP)
  viewHW(res, "m709")
  viewHW(res, "m654")
  viewHW(res, "m47")
  viewHW(res, "p46")
  viewHW(res, "p79")
  viewHW(res, "p252")
  viewHW(res, "p491")
  viewHW(res, "p523")

[Package fbat version 1.0.0 Index]