calculate_mktable: Calculate McDonald-Kreitman contingency table
In surh/HMVAR: Human Microbiome Variant Analysis in R

Description Usage Arguments Value Examples

Takes SNVs in MIDAS format and produces a McDonald-Kreitman contingency table.

1	calculate_mktable(info, freq, depth, map, depth_thres = 1, freq_thres = 0.5)

`info`	A snv x variable data frame or table. Must have columns 'site_id', 'minor_allele', 'major_allele', 'gene_id' and 'amino_acids' as defined in the midas_merge.py snps from MIDAS.
`freq`	A snv x sample data frame or tibble with minor allele frequenncies. Must have a 'site_id' column.
`depth`	A snv x sample data frame or tibble with sequence coverage. Must have a 'site_id' column.
`map`	A sample x group data frame or tibble. Must have columns 'sample' and 'Group'.
`depth_thres`	The minimum number of reads at a position in a given sample for that position in that sample to be included.
`freq_thres`	Frequency cuttoff for minor vs major allele. The value represents the distance from 0 or 1, for a site to be assigned to the major or minor allele respectively. It must be a value in [0,1].

A tibble with columns gene_id, Dn, Ds, Pn, and Ps, which correspond to the McDonald-Kreitman contingency table.

library(tidyverse)

map <- read_tsv(system.file("toy_example/map.txt", package = "HMVAR"),
                col_types = cols(.default = col_character())) %>%
  select(sample = ID, Group)

midas_data <- read_midas_data(system.file("toy_example/merged.snps/", package = "HMVAR"),
                              map = map,
                              genes = NULL,
                              cds_only = TRUE)

calculate_mktable(info = midas_data$info, freq = midas_data$freq, depth = midas_data$depth, map = map)