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Logistic Regression

This function calls Firth logistic regression.

Command examples:

atav.sh --logistic --sample PATH_TO_SAMPLE_FILE --covariate PATH_TO_COVARIATE_FILE  --out PATH_TO_OUTPUT_DIR

Command options:

--logistic: trigger Logistic Regression function.

--covariate: specify a covariate file to include all your interested samples and relevant covariates.

File Header is required: Familty ID, Individual ID, Covar1, Covar2, Covar3_cat...
The sample list in covariate file should match sample file.

--threshold-sort: specify a threshold of p-value then ATAV will output a separate file (sorted by p-value) that only include variants with lower p-value.

All the Command Options are available to use in this function.

Output:

logistic.csv

  • dominant P value
  • recessive P value
  • additive P value

Please check Output Columns for common columns.