Takes data from load_results()
and appends
columns used for plotting results.
augment_results(data, alpha)
data | data.table from |
---|---|
alpha | significance level used for hypothesis tests. |
A data.table containing the new appended results.
This function requires that this data has been loaded with
load_results()
.
It generates new columns for all columns that represent p-values generated by
analysis_association()
. One of the columns, having "_significant" as
its suffix, denotes whether or not the p-value is significant at the specified
alpha level. The other column, having "_bonferroni" as suffix, denotes whether the p-value is significant
with Bonferroni-corrected alpha level.
Furthermore, the user is prompted to decide if they want to create a column
named "causal", which denotes whether or not a SNP is truly causal for the
phenotype status of an individual. The user needs to have loaded "beta.txt"
with load_results()
in order to create this column.
Lastly, the user is prompted to decide if they want to create a column
named "LTFH_transformed", which is the estimated effect sizes of a
regression using the LT-FH phenotype transformed to the liability scale.
Transforming the effect sizes requires that the user has loaded results from
analysis_association()
with both pheno_name = "line_pheno"
and
pheno_name = "LTFH_pheno"
. These need to be laoded with load_results()
along with MAFs.txt
.