The Create Annotation Analysis Group Variable process adds a new variable named _AnalysisGroup_ to your Annotation Data Set. This variable, which defines analysis groups of markers, can be used as an annotation analysis group variable for processes such as Recode Genotypes (for collapsing rare variants), Multiple SNP-Trait Association, or P-Value Combination. Group size can be set to include a specified number of markers, or to include all markers within a positional window on a chromosome. To group by chromosome and position, these variables must be included in the Input Data Set.
One input Annotation Data Set is needed to run this process. This data set contains information, such as gene identity or chromosomal location, for each of the markers. The annotation data set used in this example, the samplemap.sas7bdat data set, is from Sample Genetic Marker Data. This data set was computer generated and includes data on four quantitative traits, 60 makers, and two candidate genes. The samplemap.sas7bdat annotation data set identifies markers, location, and gene identities for the 60 markers. A portion of this data set is illustrated below. This data set is a tall data set; each row corresponds to a different marker.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.
Output from this process includes one output data set accessed from a Results window. Refer to the Create Annotation Analysis Group Variable output documentation for detailed descriptions and guides to interpreting your results.