checkMendelian {fbat}R Documentation

Check Mendelian Errors

Description

Check Mendelian errors.

Usage

checkMendelian(geneSetObj, quiet = TRUE)

checkMendelian.default(pedObj, quiet=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
quiet print intermediate results if quiet=FALSE.

Details

check the following errors:

1
father id = subject id
2
mother id = subject id
3
could not determine if an individual is a parent or a child in a family
4
inconsistent parental sex in a family
5
parental genotypes are not compatible with childrens' genotypes in a family
6
all childrens' genotypes are missing in a family
7
inconsistent sib genotypes in a family

Value

A list with following elements:

errorFlag errorFlag=1 indicates the occurence of errors; errorFlag=0 indicates no error.
compatibleFlag compatibleFlag=0 indicates the occurence of non-compatibility; compatibleFlag=1 indicates compatibility.
nMerrMarker A $nMarkers x 1$ vector records the numbers of families with non-compatible genotypes, where $nMarkers$ is the number of markers.
nMerrFamily A $nFamily x 1$ vector records the numbers of markers with non-compatible genotypes, where $nFamily$ is the number of families.
nErrFamilySample A $nFamily x 1$ vector records the numbers of times that father id is equal to subject id or mother id is equal to subject id in a family.

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)
  checkMendelian(CAMP, quiet = TRUE)

[Package fbat version 1.4.0 Index]