missGFreq {fbat}R Documentation

Count frequencies of missing genotypes

Description

Count frequencies of missing genotypes

Usage

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

missGFreq.default(pedObj, founderOnly=TRUE)

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.

Details

Value

A matrix with the following three columns:

column 1 counts of genotypes, of which both alleles are missing.
column 2 counts of genotypes, of which the first allele is missing and the second allele is not missing.
column 3 counts of genotypes, of which the first allele is not missing and the second allele is missing.

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<-missGFreq(CAMP,founderOnly=FALSE)
  # number of missing genotypes per marker
  print(res$nMissMarkers)
  # number of missing genotypes per subject
  print(res$nMissSubjects[1:10,])

[Package fbat version 1.2.0 Index]