Create the SNPdata object — get

The function generates the input data needed for population genetics analyses using whole genome SNPs data genotyped from the malaria parasite.

get_snpdata(
  vcf_file = NULL,
  meta_file = NULL,
  output_dir = NULL,
  gof = NULL,
  gff = NULL,
  num_threads = 4L
)

Arguments

vcf_file: The path to the input VCF file (required)
meta_file: The path to the sample metadata file (required)
output_dir: The path to the folder where the output and temporary files will be stored (optional)
gof: The gene ontology annotation file (optional). If not provided, the default file obtained from the PlasmoDB # nolint: line_length_linter will be used
gff: The gene annotation file (optional). If not provided, the default file obtained from the PlasmoDB # nolint: line_length_linter will be used
num_threads: The number of threads to be used when reading in the data from the VCF file. default is 4

Value

An object of class SNPdata with the following 4 elements:

meta: A data.frame that contains the sample's metadata
details: A data.frame with the SNPs genomic coordinates, the fraction of missing data per SNP and the names and descriptions of the gene on which they are located.
GT: An integer matrix with the genotype data. 0='reference allele', 1='alternate allele', 2='mixed allele', NA='missing allele'
vcf: the full path to the VCF file from which the data is generated.

Examples

if (FALSE) { # \dontrun{
  snpdata <- get_snpdata(
    vcf_file   = system.file("extdata", "Input_Data.vcf.gz",
                             package = "mpbr"),
    meta_file  = system.file("extdata", "SampleMetadata.RDS",
                             package = "mpbr"),
    output_dir = tempdir()
 )
} # }