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Import and tidy DArT metadata.

Source: R/dart.R
tidy_dart_metadata.Rd

Used internally in radr and might be of interest for users. The function generate a tidy dataset of DArT markers and associated metadata. Usefull to filter before importing the actual dataset.

Usage

tidy_dart_metadata(
  data,
  filename = NULL,
  verbose = FALSE,
  parallel.core = parallel::detectCores() - 1
)

Arguments

data

DArT output file. Note that most popular formats used by DArT are recognised (1- and 2- row format, also called binary, and count data.). If you encounter a problem, sent me your data so that I can update the function. The function can import .csv or .tsv files.

filename

(optional) The function uses read_parquet, to write the tidy data frame in the working directory. The file extension appended to the filename provided is .arrow.parquet. With default: filename = NULL, the tidy data frame is in the global environment only (i.e. not written in the working directory...). Default: filename = NULL.

verbose

Logical indicating whether progress messages are emitted. Default: verbose = FALSE.

parallel.core

Default: parallel.core = parallel::detectCores() - 1.

Value

A tidy dataframe with these columns:

  1. MARKERS: generated by radr and correspond to CHROM + LOCUS + POS separated by 2 underscores.

  2. CHROM: the chromosome, for de novo: CHROM_1.

  3. LOCUS: the locus.

  4. POS: the SNP id on the LOCUS.

  5. REF: the reference allele.

  6. ALT: the alternate allele.

  7. CALL_RATE: call rate output specific of DArT.

  8. AVG_COUNT_REF: the coverage for the reference allele, output specific of DArT.

  9. AVG_COUNT_SNP: the coverage for the alternate allele, output specific of DArT.

  10. REP_AVG: the reproducibility average, output specific of DArT.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
clownfish.dart.tidy <- genometranslator::tidy_dart_metadata(
data = "clownfish.dart.tsv",
verbose = TRUE)
} # }