Query genotypes for one or more variant IDs from a wide-format genotype table.

Usage

query_genotypes(
  db_path,
  variant_ids,
  variant_id_col = "variant_id",
  variants_table = "variants",
  genotypes_table = "genotypes",
  meta_data = NULL
)

Arguments

db_path: The path to your SQLite or PostgreSQL database.
variant_ids: A character vector of variant IDs to query.
variant_id_col: A character value specifying the column name of variant IDs in the SQLite database.
variants_table, genotypes_table,: A character value specifying the column names of variants and genotypes tables, respectively, in the SQLite database. if the `meta_data = NULL`, it returns all the metadata in the variants table.
meta_data: A character vector of metadata to include with the genotype data.

Value

A data.frame of genotype data in variants x samples format with metadata.

Examples

# \donttest{
# example code
library(panGenomeBreedr)

# Define tempdir
path <- tempdir()

# Mini SQLite database
mini_db <-  system.file("extdata", "mini_sorghum_variant_vcf.db.gz",
                     package = "panGenomeBreedr",
                     mustWork = TRUE)

# Path to SQLite databases: INDEL and SNP
mini_db_path <- file.path(path, 'mini_sorghum_variant_vcf.db')

# Unzip compressed mini database and save in tempdir
R.utils::gunzip(mini_db,
               destname = mini_db_path,
               remove = FALSE)

# Extract all genotypes for all samples for any set of variants
geno_filter <- query_genotypes(db_path = mini_db_path,
                               variant_ids = c("INDEL_Chr05_75104541",
                                               "SNP_Chr05_75104557"),
                               meta_data = c('chrom', 'pos', 'ref', 'alt',
                                             'variant_type'))
# Clean tempdir
contents <- list.files(tempdir(),
                             full.names = TRUE,
                             recursive = TRUE,
                             all.files = TRUE,
                             include.dirs = TRUE)
unlink(contents, recursive = TRUE, force = TRUE)
# }