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Linear Regression

Special Note:

The value of the Phenotype column in the sample file should be replaced with a quantitative trait instead of the case/ctrl value. For simplicity, the options in ATAV will treat all of the samples as controls, so all the control related filter options are still working as expected & case related filter will no longer work in this function.

Command examples:

atav.sh --linear --sample PATH_TO_SAMPLE_FILE --quantitative PATH_TO_QUANTITATIVE_FILE  --out PATH_TO_OUTPUT_DIR

Command options:

--linear: trigger Linear Regression function.

--quantitative: specify a quantitative file to include all your interested samples and relevant quantitative traits.

File format: sample name and quantitative trait (tab delimiter)

--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:

allelic.csv, dominant.csv, recessive.csv, genotypic.csv

  • P value
  • Beta1

Please check Output Columns for common columns.