fbatme {fbati}

FBAT Main effects Test

Description

Family based test for the main genetic effect, using the variance based on Mendelian transmissions. The null hypothesis is that there is no linkage and no association.

Usage

fbatme( ped=NULL, phe=NULL,
        data=mergePhePed(ped,phe),
        marker=NULL,
        trait="AffectionStatus",
        model="additive",
        fixNames=TRUE,
        verbose = FALSE )

Arguments

ped

Object from (f)read.ped or as.ped. See write.ped in the pbatR R package for more details on the file format.

phe

Object from (f)read.phe or as.phe. See write.phe in the pbatR R package for more details on the file format.

data

a data.frame object containing required data, or formed from merging a pedigree and phenotype object together. The first columns of it must be as in a ‘ped’ object, while the next can be in any order representing marker or phenotype information.

marker

Default is NULL for all markers. Otherwise, it can be the names of the marker (if you load in with read.ped, this should be without the '.a'/'.b' added to differentiate the two markers). If you are using more specialized loading routines, this represents the numbers of the columns where the markers are at. For example, 7:10 would mean that columns 7 and 8 represent one locus, and columns 9 and 10 represent another locus.

trait

Character string representing the name of the trait variable to use (a column header name of the 'data' parameter).

model

one of "additive", "dominant", or "recessive".

fixNames

Just leave this to TRUE if creating from ped/phe objects (pops off the '.a' and '.b' added on to the names of the two markers that are added on when read in via the (f)read.ped(...) routine).

verbose

Developer use only (extended output).

Details

Returns a data.frame object with the results. Uses the variance based on Mendelian transmissions.

NOTE: The allele frequency is simply based on the allele frequency in all genotyped individuals, and is not the best choice.