The Marker Statistics report enables you to explore several properties of all biallelic markers in a data set. The process calculates various single marker measures and various measurements of linkage disequilibrium.
The Marker Statistics red triangle contains the following options:
Levels Table
Select this option to view the Levels Table. The Levels Table indicates the number of genotypes that are observed for each marker.
Counts Table
Select this option to view the Counts Table. The Counts Table indicates the number of individuals exhibiting each genotype for each marker.
Result Table
Select this option to view the Result Table.
PValue Plot
Select this option to view the Hardy-Weinberg Equilibrium FDR Logworth Plot.
LD Decay Plot
Select this option to view the LD Decay Plot.
Note: This option is available when one or more With Markers are specified.
Save Result Table
Use this option to save the Result Table as a JMP table.
Save Proportion of Missing Markers
Use this option to add a column to the original data table that contains the proportion of missing markers in each row.
Select Where
Use this option to subset the Result Table based on specified criteria.
Recode Marker
Use this option to recode all of the selected marker columns in the original data table by switching the major and minor alleles.
Select and Recode Marker
Use this option to enter a valid selection criterion for the markers to be recoded. Enter the selection criterion, click OK, and the recode system is swapped (minor to major or vice versa) for the selected markers.
Select Columns
Select a row in the Result Table and then use this option to select the corresponding columns in the original data table.