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
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"))
}