calculate_dos: Calculate Direction of Selection
In surh/HMVAR: Human Microbiome Variant Analysis in R

Calculates the Direction of Selection (DoS) statistic from McDonald-Kreitman contingency tables.

1	calculate_dos(dat, test = TRUE, clean = TRUE)

`dat`	A gene by substitution type data frame or tibble. Each row must correspond to a gene and it must have columns Dn, Ds, Pn and Ps, corresponding to the McDonald-Kreitman contingency table of each gene.
`test`	It TRUE, a Z-test will be performed on the DoS statistic.
`clean`	If TRUE, genes where DoS is undefined (either Dn and Ds are both zero, or Pn and Ps are both zero), will be removed from the result.

A tibble with the same columns as Dat plus a column named DoS. If test is passed, a column named p.value will also be included unless such a column already exists. In that case a column with the name DoS.p.value will be included

surh/HMVAR documentation built on Aug. 18, 2021, 1:21 a.m.