pedFlagHomo {fbat}R Documentation

flag homo/heterozygotes

Description

Flag homo/heterozygotes.

Usage

pedFlagHomo(geneSetObj, founderOnly=TRUE, quiet=FALSE)

pedFlagHomo.default(pedObj, 
            founderOnly=TRUE,
            quiet=FALSE)

Arguments

geneSetObj a geneSet object.
pedObj a list with five elements: ped, columns, markerNames, Position, and filename. ped is a 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 are the 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"); founderOnly indicates if using only founder info; markerNames is a vector of marker names; Position is a vector of marker positions; fileName is the pedigree file name
founderOnly indicates if using only founder info
quiet print intermediate results if quiet=FALSE.

Value

countMat Count the number of homo/heterozygotes.
flagHomoMat Flag homo/heterozygotes. 1 – homozygotes; 0 – heterozygotes; -1 – genotype contains one missing allele; -2 – genotype contains two missing alleles.
markerNames marker names.

Author(s)

Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu, Gregory Warnes warnes@bst.rochester.edu, Nitin Jain nitin.jain@pfizer.com

Examples

  data(CAMP)
  res<-pedFlagHomo(CAMP)
  res$countMat
  res$flagHomoMat
  res$markerNames

[Package fbat version 1.4.0 Index]