This process standardizes numerically coded
genotypes
to have a genetic
mean
of zero and a genetic
variance
of one. This is useful prior to predictive modeling in order to let each genotype have an equal effect on the response. The process also optionally imputes
missing values
with zeros.
One
Input Data Set
, containing all of the marker data is needed for this process. The sample data set used in the following example, the
samplegmdata_numgeno
data set, is partially shown below.
The original
samplegmdata
data set described in
Data Sets Used in JMP Genomics Processes
was computer generated and consists of 1000 rows of individuals with 130 columns corresponding to data on these individuals. Marker data is presented in the two-column
allelic
format. This data set was recoded using the
Recode Genotypes
process to generate
samplegmdata_numgeno
data set. The recoded data set consists of 611 rows with 70 columns. Marker data is presented as
numeric variables
in the one-column genotypic format.
Note
:
The
marker variables
in the input data set must contain numerically coded genotypes; a data set containing these can be obtained by checking the
Create data set with numerically coded genotypes
option when you run
Marker Properties
or by running the
Recode Genotypes
process.
This process generates a new output data set containing the standardized genotypes. Refer to the
Standardize Genotypes
output documentation for detailed descriptions of the output of this process.