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_genotype,
  file_type = "pedmap",
  biome_id_column = "ind_id",
  threshold = 0.05,
  ind_selected = NULL
)

Arguments

path_to_microbiome

String giving the path to count table file. "path/to/microbiome.{extension}"

path_to_genotype

String giving the path and prefix to the genotype file. This should be one of "pedmap" or "vcf". (default: "pedmap"), see file_type param. For a "example_pedmap.ped" file enter only "path/to/example_pedmap".

file_type

String specifying the file type used to load genotype data. This should be one of "pedmap" or "vcf". (default: "pedmap").

biome_id_column

String specifying the name of the column containing the individual IDs for the microbiome matrix. Default is "ind_id".

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 list containing two object. A matrix containing the microbiome(microbiome). A list from MoBPS package, containing the genotypes (population). Individuals are in columns and taxa or SNPs are in rows.

Note

The number of individuals in the microbiome an genotype data must be equivalent.

See also

generate_founder(), rarefied_microbiome()

Examples

if (FALSE) { # \dontrun{
# Create founder object from PED/MAP set
founder_object <- read_input_data(path_to_microbiome = "/path/to/microbiome.txt",
                                  path_to_pedmap = "/path/to/pedmap/'prefix'",
                                  biome_id_column = "ind_id",
                                  threshold = 0.05,
                                  ind_selected = NULL,
                                  file_type = "pedmap")

# Create founder object from VCF
founder_object <- read_input_data(path_to_microbiome = "/path/to/microbiome.txt",
                                  path_to_pedmap = "/path/to/vcf/'prefix'",
                                  biome_id_column = "ind_id",
                                  threshold = 0.05,
                                  ind_selected = NULL,
                                  file_type = "vcf")
} # }