R: fbatj

fbatj {fbati}

R Documentation

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