Formatting of ped and map files into haplotypes table and filter individuals

Formatting of ped and map files into haplotypes table and filter individuals

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

Value

Matrix of taxa (in columns) accross individuals (in rows), genotypes of each generation are reachable thanks to "population" attribute. Genotypes are encodes as 0,1,2 and generated using the MoBPS package.

See also

read_input_data(), rarefied_microbiome()

Examples

if (FALSE) { # \dontrun{
  microbiome <- data.table::fread("/path/to/microbiome.txt")
  founder_object <- generate_founder(path = "/path/to/pedmap", microbiome) 
} # }