GxE.scan
.
id.var
and response.var
).
No default.file
.
See the individual model documentation for the allowable stratifications.
The default is NULL so that all observations
belong to the same strata.file
that will be included in the model as main effects.
The default is NULL.file
that will be included in the model as interactions with each SNP
in the genotype data.
The default is NULL.save()
function. 3 is for a table that will be read in
with read.table()
. 4 is for a SAS data set.
The default is 3.file
.
The default is "".na.strings
in read.table()
.
The default is "NA".cc.var
variable used in snp.matched
.
The default is NULL.nn.var
variable used in snp.matched
.
The default is NULL.file
, id.var
, and response.var
must be specified.
The variable id.var
is the link between the covariate data and the genotype data.
For each subject id, there must be the same subject id in the genotype data for that subject
to be included in tha analysis. If the genotype data is in a PLINK format, then id.var
must be of length 2 corresponding the the family id and subject id. Missing data: If any of the variables defined in main.vars
, int.vars
,
strata.var
, or response.var
contain missing values, then those subjects
will be removed from the covariate and outcome data. After the subjects with missing values
are removed, the subject ids are matched with the genotype data.