Generate markers metadata

Generate markers metadata: CHROM, LOCUS, POS, REF, ALT when missing from tidy datasets.

generate_markers_metadata(
  data,
  generate.markers.metadata = TRUE,
  generate.ref.alt = FALSE,
  biallelic = NULL,
  parallel.core = parallel::detectCores() - 1,
  verbose = TRUE
)

Arguments

data

An object with a column named MARKERS. If CHROM, LOCUS, POS are already present, the function returns the dataset untouched. The data can be whitelists and blacklists of markers or tidy datasets or radiator GDS object.

generate.markers.metadata

(logical, optional) Generate missing markers metadata when missing. "CHROM", "LOCUS", "POS". Default: generate.markers.metadata = TRUE

generate.ref.alt

(logical, optional) Generate missing REF/ALT alleles with: REF = A and ALT = C (for biallelic datasets, only). It is turned off automatically when argument markers.meta.lists.only = TRUE and on automatically when argument markers.meta.all.only = TRUE Default: generate.ref.alt = FALSE

biallelic

(logical) Speed up the function execution by entering if the dataset is biallelic or not. Used internally for verification, before generating REF/ALT info. By default, the function calls detect_biallelic_markers. The argument is required if data is a tidy dataset and not just a whitelist/blacklist. Default: biallelic = NULL

parallel.core

(optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

verbose

(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

Value

Depending on argument's value, the same data is returned in the global environment, with potential these additional columns: CHROM, LOCUS, POS, REF, ALT.

See also

detect_biallelic_markers and separate_markers

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
tidy.data <- radiator::generate_markers_metadata(data = bluefintuna.data)
} # }