QBMS (version 1.5.0)

gigwa_get_variants: Get Available Variants in the Selected GIGWA Run

Description

Retrieve variant data (e.g., SNP markers) for the selected GIGWA run based on filtering criteria, including minor allele frequency, missing data threshold, and sample subset.

Usage

gigwa_get_variants(
  max_missing = 1,
  min_maf = 0.5,
  samples = NULL,
  start = NULL,
  end = NULL,
  referenceName = NULL
)

Value

A data frame where the first 4 columns describe the SNP (rs# variant name, alleles, chrom, pos), and subsequent columns contain numerical genotyping information (0 for reference allele, 1 for heterozygous, and 2 for minor allele).

Arguments

max_missing

The maximum allowable missing data ratio, between 0 and 1 (default is 1, meaning up to 100% missing data).

min_maf

Minimum Minor Allele Frequency (MAF) between 0 and 0.5 (default is 0).

samples

A list of sample names to include in the query (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).

referenceName

The reference sequence name (e.g., chromosome).

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")
  marker_matrix <- gigwa_get_variants(max_missing = 0.2, 
                                      min_maf = 0.35, 
                                      samples = c("ind1", "ind3", "ind7"))
}