Fetches genotype data from a BrAPI server and converts it into a numeric
dosage matrix (samples × markers) compatible with genomic selection
packages like rrBLUP, BGLR, and sommer.
Arguments
- con
A
brapi_connection()object.- variantSetDbId
Character. The variant set to retrieve.
- sep
Character. Unphased allele separator. Default
"/"(e.g."0/1"). Phased calls using"|"are also handled automatically.- unknown_string
Character. String representing missing data. Default
".".
Value
A numeric (double) matrix: rows = samples (callSetDbIds),
columns = markers (variantDbIds). Values are whole-number dosages
(0, 1, 2 for diploids; 0–N for polyploids). Missing calls are NA.
Details
The server is asked for expanded homozygotes, sep as the unphased
separator and unknown_string for missing data. Allele dosage is then
computed by splitting each genotype string on sep (or "|" for phased
calls) and counting how many alleles are non-reference (i.e. not "0").
A call with any missing allele (unknown_string, "." or ""), such as
"./1", becomes NA. A server that still collapses a homozygote to a
single allele ("1") gets it expanded to the ploidy seen in the rest of
the data, or to 2 if every call is collapsed. Alleles must be numeric
indices ("0", "1", ...); nucleotide calls such as "A/T" are an
error.
BrAPI endpoint
GET /allelematrix - see the
v2.1 specification.
Examples
# \donttest{
con <- brapi_connection("https://test-server.brapi.org")
if (brapi_ping(con)) {
dosage <- brapi_get_dosage_matrix(con, "variantset1")
dim(dosage)
# Use with rrBLUP:
# library(rrBLUP)
# result <- mixed.solve(y = pheno$yield, Z = dosage)
}
#> ✔ Server <https://test-server.brapi.org> is reachable.
#> ℹ Fetching allele matrix for variant set "variantset1"...
#> ℹ Encoding 260 genotype calls as allele dosages...
#> ✔ Dosage matrix ready: 13 samples x 20 markers.
#> [1] 13 20
# }