Right now its a little confusing because I've mixed how I handle this distinction in different parts of the package.
Sometimes I have a flag "pvals.in.log" that will change the PVAL column to -log10(pvalue) if its not already. This is a little confusing because it means the column name PVAL can contain logpvalues as well.
Other parts of the package I explicitly ask for a LOGPVAL column.
I need to decide on 1 to use but it won't be fun! ¯\(ツ)/¯
Right now its a little confusing because I've mixed how I handle this distinction in different parts of the package.
Sometimes I have a flag "pvals.in.log" that will change the PVAL column to -log10(pvalue) if its not already. This is a little confusing because it means the column name PVAL can contain logpvalues as well.
Other parts of the package I explicitly ask for a LOGPVAL column.
I need to decide on 1 to use but it won't be fun! ¯\(ツ)/¯