gigwa_get_variants: Get Available Variants in the Selected GIGWA Run

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

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
)

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).

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).

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

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