Convert PCAWG Identifiers — convert

Run data("pcawg_full") or data("pcawg_simple") to see detail database for conversion. The pcawg_simple database only contains PCAWG white-list donors.

Usage

convert_pcawg(
  x,
  from = "icgc_specimen_id",
  to = "icgc_donor_id",
  db = c("full", "simple"),
  multiple = FALSE
)

Arguments

x: A character vector to convert.
from: Which identifier type to be converted. For db "full", one of donor_unique_id, submitter_donor_id, icgc_donor_id, aliquot_id, submitter_specimen_id, icgc_specimen_id, submitter_sample_id, icgc_sample_id. For db "simple", one of tumour_specimen_aliquot_id, normal_specimen_aliquot_id, donor_unique_id, submitted_donor_id, icgc_donor_id, icgc_sample_id, icgc_specimen_id, submitted_specimen_id, submitted_sample_id, tcga_specimen_uuid, tcga_sample_uuid, tcga_donor_uuid.
to: Identifier type convert to. Same as parameter from.
db: Database, one of "full" (for data("pcawg_full")) or "simple" (for data("pcawg_simple")).
multiple: if TRUE, return a data.table instead of a string vector, so multiple identifier mappings can be kept.

Value

A character vector.

Examples

# \donttest{
x <- convert_pcawg("SP1677")
x
#> [1] "DO804"

y <- convert_pcawg("DO804",
  from = "icgc_donor_id",
  to = "icgc_specimen_id", multiple = TRUE
)
y
#>      from     to
#>    <char> <char>
#> 1:  DO804 SP1682
#> 2:  DO804 SP1677
# }
if (FALSE) { # \dontrun{
convert_pcawg("SA5213")
} # }