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 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")

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")
} # }