gigwa_get_variants {QBMS}

Get Available Variants in the Selected GIGWA Run

Description

Query the variants (e.g., SNPs markers) in the selected GIGWA run that match a given criteria.

Usage

gigwa_get_variants(
  max_missing = 1,
  min_maf = 0,
  samples = NULL,
  start = NULL,
  end = NULL,
  referenceName = NULL
)

Arguments

max_missing

Maximum missing ratio (by sample) between 0 and 1 (default is 1 for 100%).

min_maf

Minimum Minor Allele Frequency (MAF) between 0 and 1 (default is 0 for 0%).

samples

A list of samples subset (default is NULL, which will retrieve for all samples).

start

Start position of region (zero-based, inclusive) (e.g., 19750802).

end

End position of region (zero-based, exclusive) (e.g., 19850125).

referenceName

Reference sequence name (e.g., '6H' in the Barley LI-AM).

Value

A data.frame that has the first 4 columns describing attributes of the SNP (rs#: variant name, alleles: reference allele / alternative allele, chrom: chromosome name, and pos: position in bp), while the following columns describe the SNP value for a single sample line using numerical coding 0, 1, and 2 for reference, heterozygous, and alternative/minor alleles.

Author(s)

Khaled Al-Shamaa, [e-mail]

Examples

if (interactive()) {
  # Configure your GIGWA connection
  set_qbms_config("https://gigwa.southgreen.fr/gigwa/", 
                  time_out = 300, engine = "gigwa", no_auth = TRUE)

  # Select a database by name
  gigwa_set_db("Sorghum-JGI_v1")

  # Select a project by name
  gigwa_set_project("Nelson_et_al_2011")
  
  # Select a specific run by name
  gigwa_set_run("run1")
  
  marker_matrix <- gigwa_get_variants(max_missing = 0.2, 
                                      min_maf = 0.35, 
                                      samples = c("ind1", "ind3", "ind7"))
}