Map input to cell identifiers

Usage

mapCells(object, ...)

# S4 method for Cellosaurus
mapCells(
  object,
  cells,
  keyType = c("cellosaurusId", "depmapId", "sangerModelId", "atccId", "cellLineName"),
  strict = FALSE
)

Arguments

object

character. Cell names (or Cellosaurus accession identifiers).

cells

character. Cell identifiers.

keyType

character(1). Identifier format to return.

strict

logical(1).

FALSE, return NA for cell lines that fail to map.
TRUE: Error on mapping failure.

...

Additional arguments.

Value

Named character. User input in the names and Cellosaurus accession identifiers in the values.

Details

This function is designed to take input from a spreadsheet, electronic laboratory notebook entry, or cell line provider, where the cell line names may be inconsistent.

If you notice any mapping errors, please file a bug report.

Note

Updated 2023-09-22.

Examples

data(cello)

## Cellosaurus ====
object <- cello
cells <- head(cello[["cellLineName"]])
print(cells)
#> character-Rle of length 6 with 6 runs
#>   Lengths:       1       1       1       1       1       1
#>   Values :   "HEL" "HL-60" "HMC-1" "K-562"   "NB4" "THP-1"
cells <- mapCells(object = object, cells = cells)
print(cells)
#>         HEL       HL-60       HMC-1       K-562         NB4       THP-1 
#> "CVCL_0001" "CVCL_0002" "CVCL_0003" "CVCL_0004" "CVCL_0005" "CVCL_0006"