gigwa_get_allelematrix: Get Markers Matrix in the Selected GIGWA Run

In icarda-git/QBMS: Query the Breeding Management System(s)

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
)

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).

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).

Author(s)

Khaled Al-Shamaa, [e-mail]

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])
}

icarda-git/QBMS documentation built on Sept. 25, 2024, 10:45 p.m.