Retrieve a two-dimensional matrix of genotype data from the selected GIGWA run. This matrix is returned based on filters for regions, samples, or variants. The data can be simplified to use numeric coding for genotypes, or returned in its raw VCF-like format.
Usage
gigwa_get_allelematrix(
samples = NULL,
start = 0,
end = "",
chrom = NULL,
snps = NULL,
snps_pageSize = 10000,
samples_pageSize = 100,
simplify = TRUE
)Arguments
- samples
A list of sample names to include (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).
- chrom
Reference sequence name (e.g., chromosome or contig).
- snps
A list of variant names to filter (optional).
- snps_pageSize
Number of variants to fetch per page (default is 10,000).
- samples_pageSize
Number of samples to fetch per page (default is 100).
- simplify
Whether to simplify the returned data using numeric coding (default is TRUE).
Value
A data frame with rows representing SNP markers and columns representing samples. Values are numeric codings (0: reference allele, 1: heterozygous, 2: alternative 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")
samples <- gigwa_get_samples()
chroms <- gigwa_get_sequences()
geno_data <- gigwa_get_allelematrix(samples = samples[1:5],
start = 0,
end = 1234567,
chrom = chroms[1:3])
}