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Extract DArT TARGET_ID

Source: R/dart.R
extract_dart_target_id.Rd

Extracts DArT TARGET_ID from a DArT file to help build a STRATA file. Optionally extracts the DArT metadata block.

DArT metadata are not fully consistent across files (fields present and ordering may vary and are not always documented). When metadata are requested, the function uses a conservative strategy:

  • TARGET_ID is always identified (stable DArT position)

  • PLATE_WELL, WELL_ROW, WELL_COL are detected when possible

  • remaining metadata are named DART_METADATA_*

Possible DArT metadata fields may include:

  • DART_NUMBER

  • DART_PLATE_BARCODE

  • SAMPLE_COMMENTS

  • WELL_ROW

  • WELL_COL

  • CLIENT_PLATE_BARCODE

  • CLIENT_ID

If known, metadata column names can be supplied using metadata.colnames.

Usage

extract_dart_target_id(
  data,
  write = TRUE,
  metadata = FALSE,
  metadata.colnames = NULL
)

Arguments

data

(file) 6 files formats used by DArT are recognized by radr. Don't modify the DArT file, to do this, use the strata file/argument below. The function can import files ending with .csv or .tsv.

  1. 1row: Genotypes are in 1 row and coded (0, 1, 2, -). 0 for 2 reference alleles REF/REF, 1 for 2 alternate alleles ALT/ALT, 2 for heterozygote REF/ALT, - for missing.

  2. 2rows: No genotypes. It's absence/presence, 0/1, of the REF and ALT alleles. Sometimes called binary format.

  3. counts: No genotypes, It's counts/read depth for the REF and ALT alleles. Sometimes just called count data. This should be the preferred file format, because DArT output the coverage (read depth for each genotypes).

  4. silico.dart: SilicoDArT data. No genotypes, no REF or ALT alleles. It's a file coded as absence/presence, 0/1, for the presence of sequence in the clone id.

  5. silico.dart.counts: SilicoDArT data. No genotypes, no REF or ALT alleles. It's a file coded as absence/presence, with counts for the presence of sequence in the clone id.

  6. dart.vcf: For DArT VCFs, please use read_vcf.

If you encounter a problem, sent me your data so that I can update the function.

write

(logical) Default: TRUE. Write extracted TARGET_ID table.

Default: write = TRUE.

metadata

(logical) Default: FALSE. Extract metadata when present.

Default: metadata = FALSE.

metadata.colnames

(character, optional) Metadata column names excluding TARGET_ID. Length must match number of metadata columns. With the default, (automatic conservative naming).

Default: metadata.colnames = NULL.

Value

A tidy dataframe with TARGET_ID and optional metadata. TARGET_ID are cleaned using clean_ind_names(): spaces and commas removed, _ and : replaced by -, converted to upper case.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{

# Extract TARGET_ID only
genometranslator::extract_dart_target_id("mt.dart.file.csv")

# Extract metadata with automatic naming
genometranslator::extract_dart_target_id(
  data = "mt.dart.file.csv",
  metadata = TRUE
)

# Extract metadata with user naming
genometranslator::extract_dart_target_id(
  data = "mt.dart.file.csv",
  metadata = TRUE,
  metadata.colnames = c(
    "DART_NUMBER",
    "DART_PLATE_BARCODE",
    "CLIENT_PLATE_BARCODE",
    "WELL_ROW",
    "WELL_COL",
    "SAMPLE_COMMENTS"
  )
)

# Build STRATA file
strata <- genometranslator::extract_dart_target_id("mt.dart.file.csv") %>%
  dplyr::mutate(
    INDIVIDUALS = TARGET_ID,
    STRATA = "POP1"
  )

} # }