fbatj: fbatj

In fbati: Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families

fbatj

Description

Family based joint test for both the main effect of the gene and gene-environment interaction, command/line or GUI (provide no options to start gui, i.e. just type fbatj() and press return). Null hypothesis is no linkage and no association.

Usage

fbatj( ped=NULL, phe=NULL,
       data=mergePhePed(ped,phe),
       marker = NULL,
       trait = "AffectionStatus",
       env = "env",
       model = "additive",
       mode = "univariate",
       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).
env	Character string representing the name of the environmental variable to use (a column header name of the 'data' parameter).
model	one of "additive", "dominant", or "recessive".
mode	"univariate" is the only one supported.
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 variance based on Mendelian transmissions (no longer uses the empirical variance).

For an example, see the fbati function.

References

K Lunetta, S V Faraone, J Biederman, and N M Laird. Family-based tests of association and linkage that use unaffected sibs, covariates, and interactions. Am J Hum Genet, 2000, 66, 605-614.

See Also

fbatj

fbati documentation built on Feb. 16, 2023, 9:31 p.m.