Analysis keywords
| Keyword | Default Value | Allowed value | Description |
|---|---|---|---|
kinship_output_file | KinshipOutputFile.txt | true/false | OpenMendel generated output file with table of kinship coefficients |
repetitions | 1 | Integer | Repetitions for sharing statistics |
xlinked_analysis | false | beelean | Whether markers are on the X chromosome |
compare_kinships | false | boolean | Whether we want to compare theoretical vs empiric kinship |
kinship_plot | "" | User defined file name | A user specified name for a plot comparing theoretical and empiric kinship value |
z_score_plot | "" | User defined file name | A user specified name for a plot of fisher's z statistic. |
grm_method | MoM | GRM, MoM, Robust | Method used for empiric kinship calculation. Defaults to MoM, but user could choose the more common GRM or Robust GRM methods instead. (Warning: Based on our experience, Fisher's z score is very unreliable if the GRM method is used for rare (maf < 0.2) snps) |
maf_threshold | 0.01 | Real number between 0 and 1 | The minor allele frequency threshold for the GRM computation |
deviant_pairs | false | Integer less than $n(n+1)/2$ | Number of top deviant pairs (theoretical vs empiric kinship) the user wants to keep |
See also
- MendelBase documentation for general keywords common to most analysis package
- Old MendelKinship documentation