Formatting of ped/map files or vcf into haplotypes table and add it inside the founder_object list.

Formatting of ped/map files or vcf into haplotypes table and add it inside the founder_object list.

Usage

generate_founder(path = NULL, microbiome_matrix, file_type = "pedmap")

Arguments

path

String giving the path and prefix to ped and map file

microbiome_matrix

Filtered microbiome matrix, with OTUs in columns and individuals in rows

file_type

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

Value

A list of two matrix. The microbiome matrix contains taxa (in columns) accross individuals (in rows). The population object contains genotypes, encoded as 0,1,2 and generated using the MoBPS package.

See also

read_input_data(), rarefied_microbiome()

Examples

if (FALSE) { # \dontrun{
  # Generate founder object from PED/MAP set
  microbiome <- data.table::fread("/path/to/microbiome.txt")
  founder_object <- generate_founder(path = "/path/to/pedmap", microbiome, file_type = "pedmap")
  
  # Generate founder object from VCF set
  microbiome <- data.table::fread("/path/to/microbiome.txt")
  founder_object <- generate_founder(path = "/path/to/vcf", microbiome, file_type = "vcf") 
} # }