read_input_data: read sequence data from file to be used in simulation

In thijsjanzen/GenomeAdmixR: Simulate Admixture of Genomes

read sequence data from file to be used in simulation

Description

Create data in a format that can be used by GenomeAdmixR

Usage

read_input_data(
  file_names,
  type,
  chosen_chromosome,
  number_of_snps = NA,
  random_snps = TRUE,
  verbose = FALSE
)

Arguments

file_names	names of input files
type	type of data, options are 'ped' and 'vcf'
chosen_chromosome	GenomeAdmixR simulates only a single chromosome.
number_of_snps	number of snps to be loaded from file, default is to load all snps
random_snps	if a subset of all snps has to be taken, should these be sampled sequentially (e.g. the first 100 snps) or randomly (100 randomly sampled snps) (examples are for 'number_of_snps' = 100).
verbose	give verbose output

Value

list with two properties: genomes a matrix with the sequence translated to numerics, such that [actg] corresponds to [1234], and missing data is represented with "-". Rows in the matrix correspond to chromosomes, and columns represent bases. Two consecutive rows represent an individual, such that rows 1-2 are individual, rows 3-4 are one individual etc. markers corresponds to the locations of the markers (in bp) on the chosen chromosome.

thijsjanzen/GenomeAdmixR documentation built on Feb. 16, 2024, 7:27 p.m.