fbatj {fbati} | R Documentation |
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).
fbatj( ped=NULL, phe=NULL, data=mergePhePed(ped,phe), marker = NULL, trait = "AffectionStatus", env = "env", model = "additive", mode = "univariate", fixNames = TRUE, verbose = FALSE )
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). |
Returns a data.frame object with the results. Uses the empirical variance.
For an example, see the fbati function.
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.