pedAFreq {fbat}R Documentation

get allele frequencies

Description

Get allele frequencies (missing alleles allowed).

Usage

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

pedAFreq.default(pedObj, 
         founderOnly=TRUE,
         missingOutput=FALSE,
         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.
missingOutput indicates if missing allele frequency should be output.
quiet print intermediate results if quiet=FALSE.

Value

aFreqMat allele frequencies.
aPercMat allele percentages.
missingOutput indicates if missing allele frequency should be output.

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

[Package fbat version 1.2.0 Index]