Get Markers Map in the Selected GIGWA Run — gigwa_get

Retrieve a filtered list of SNP variants from the selected run. This function allows users to query variants based on chromosomal regions and return results in simplified format.

Usage

gigwa_get_markers(start = NULL, end = NULL, chrom = NULL, simplify = TRUE)

Arguments

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).
simplify: Logical, if TRUE (default) returns data in a simplified HapMap-like format with columns for rs#, alleles, chromosome, and position.

Value

A data frame of SNP markers, optionally simplified to include rs#, alleles, chromosome, and position.

Author

Khaled Al-Shamaa (k.el-shamaa@cgiar.org)

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")
  chroms <- gigwa_get_sequences()
  geno_map <- gigwa_get_markers(start = 0, end = 12345678, chrom = chroms[7])
}