mkvalues: Entries in McDonald-Kreitman table.

In surh/HMVAR: Human Microbiome Variant Analysis in R

Description

Calculates the four entries (Dn, Ds, Pn, Ps) in the McDonald-Kreitman contingency table.

Usage

mkvalues(info)

Arguments

info	A data table corresponding to the MIDAS snps_info.txt output file. Must have been processed with determine_snp_effect and determine_snp_dist, and so it must contain columns 'snp_effect' and 'distribution'

Value

A tibble with one column with the count of each substitution type.

Examples

library(HMVAR)

# Get file paths
midas_dir <- system.file("toy_example/merged.snps/", package = "HMVAR")
map <- readr::read_tsv(system.file("toy_example/map.txt", package = "HMVAR"),
                       col_types = readr::cols(.default = readr::col_character())) %>%
  dplyr::select(sample = ID, Group)

# Read data
midas_data <- read_midas_data(midas_dir = midas_dir, map = map, cds_only = TRUE)

info <- determine_snp_effect(midas_data$info) %>%
  determine_snp_dist(freq = midas_data$freq,
                     depth = midas_data$depth, map = map,
                     depth_thres = 1, freq_thres = 0.5)
info

mktable <- info %>%
  split(.$gene_id) %>%
  purrr::map_dfr(mkvalues,
                 .id = "gene_id")
mktable

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