gigwa_get_variants {QBMS} | R Documentation |
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, 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")
marker_matrix <- gigwa_get_variants(max_missing = 0.2,
min_maf = 0.35,
samples = c("ind1", "ind3", "ind7"))
}