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
Khaled Al-Shamaa, k.el-shamaa@cgiar.org
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"))
}