extract_markers_metadata — extract_markers_metadata • genometranslator

Import markers metadata from a genometranslator or SeqArray GDS.

Usage

extract_markers_metadata(
  gds,
  markers.meta.select = NULL,
  metadata.node = TRUE,
  whitelist = FALSE,
  blacklist = FALSE,
  verbose = FALSE
)

gds: The GDS object (genometranslator, legacy radiator, or SeqArray).
markers.meta.select: (optional, character) Names of metadata fields to import. For package GDS files, these are the column names in the metadata node. For plain SeqArray GDS, standardized names VARIANT_ID, CHROM, LOCUS, POS are mapped to variant.id, chromosome, annotation/id, position. Default: markers.meta.select = NULL.
metadata.node: (logical) Whether to prefer the package metadata node if present. Both genometranslator and legacy radiator nodes are supported. If the node is missing or empty, the function falls back to SeqArray nodes. Default: metadata.node = TRUE.
whitelist: (logical) If TRUE and a FILTERS column is present, only rows with FILTERS == "whitelist" are returned. Default: whitelist = FALSE.
blacklist: (logical) If TRUE and a FILTERS column is present, only rows with FILTERS != "whitelist" are returned. Default: blacklist = FALSE.
verbose: Logical indicating whether progress messages are emitted. Default: verbose = FALSE.