QBMS (version 1.5.0)

gigwa_get_allelematrix: Get Markers Matrix in the Selected GIGWA Run

Description

Retrieve a two-dimensional matrix of genotype data from the selected GIGWA run. This matrix is returned based on filters for regions, samples, or variants. The data can be simplified to use numeric coding for genotypes, or returned in its raw VCF-like format.

Usage

gigwa_get_allelematrix(
  samples = NULL,
  start = 0,
  end = "",
  chrom = NULL,
  snps = NULL,
  snps_pageSize = 10000,
  samples_pageSize = 100,
  simplify = TRUE
)

Value

A data frame with rows representing SNP markers and columns representing samples. Values are numeric codings (0: reference allele, 1: heterozygous, 2: alternative allele).

Arguments

samples

A list of sample names to include (optional). If NULL, all samples will be included.

start

Start position of the query region (zero-based, inclusive).

end

End position of the query region (zero-based, exclusive).

chrom

Reference sequence name (e.g., chromosome or contig).

snps

A list of variant names to filter (optional).

snps_pageSize

Number of variants to fetch per page (default is 10,000).

samples_pageSize

Number of samples to fetch per page (default is 100).

simplify

Whether to simplify the returned data using numeric coding (default is TRUE).

Author

Khaled Al-Shamaa,

Examples

if (interactive()) {
  set_qbms_config("https://gigwa.southgreen.fr/gigwa/", 
                  time_out = 300, engine = "gigwa", no_auth = TRUE)
  gigwa_set_db("Sorghum-JGI_v1")
  gigwa_set_project("Nelson_et_al_2011")
  gigwa_set_run("run1")
  samples <- gigwa_get_samples()
  chroms <- gigwa_get_sequences()
  geno_data <- gigwa_get_allelematrix(samples = samples[1:5],
                                      start   = 0,
                                      end     = 1234567,
                                      chrom   = chroms[1:3])
}