fbatme {fbati} | R Documentation |
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.
fbatme( ped=NULL, phe=NULL,
data=mergePhePed(ped,phe),
marker=NULL,
trait="AffectionStatus",
model="additive",
fixNames=TRUE,
verbose = FALSE )
ped |
Object from |
phe |
Object from |
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 |
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 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.