pedAFreq {fbat}R Documentation

get allele frequencies

Description

Get allele frequencies (missing alleles allowed).

Usage

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

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

Arguments

geneSetObj a geneSet object.
ped pedigree data frame whose first 6 columns are pid (pedigree id), id (individual id), fid (father id), mid (mother id), sex, aff (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","affect") or equal to c("family","pid","father","mother","sex")
founderOnly indicates if using only founder info
quiet print intermediate results if quiet=FALSE.

Value

aFreqMat allele frequencies.
aPercMat allele percentages.

Author(s)

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

Examples

  data(CAMP)
  res<-pedAFreq(CAMP)
  res$aFreqMat
  res$aPercMat

[Package fbat version 1.0.0 Index]