Formatting data from file paths to base population object

Formatting data from file paths to base population object

Usage

read_input_data(
  path_to_microbiome,
  path_to_pedmap,
  threshold = 0.05,
  ind_selected = NULL
)

Arguments

path_to_microbiome

String giving the path to count table file

path_to_pedmap

String giving the path and prefix to ped and map file

threshold

Threshold for rarefaction, DEFAULT = 0.05

ind_selected

Vector of string values with individuals to keep, have to match rownames of count table file, DEFAULT = NULL

Value

A data.frame corresponding to (rarefied) microbiome with individuals in rows and taxa in columns. Genotypes data.frame is an attribute called "population" reachable using attr(output_name,"population")