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Get, set, or reset identifiers for one or all identifier field(s)

Source: R/identifiers.R
identifiers.Rd

Get, set, or reset the expected identifier(s) for one or all identifier field(s). Identifiers are used by the gDR processing functions to identify which columns in a data.table correspond to certain expected fields. Functions of the family *et_identifier will look for identifiers from the environment while functions of the family *et_SE_identifiers will look for identifiers in the metadata slot of a SummarizedExperiment object. See details for expected identifiers and their definitions.

Usage

get_env_identifiers(k = NULL, simplify = TRUE)

get_prettified_identifiers(k = NULL, simplify = TRUE)

set_env_identifier(k, v)

reset_env_identifiers()

Arguments

k

String corresponding to identifier name.

simplify

Boolean indicating whether output should be simplified.

v

Character vector corresponding to the value for given identifier k.

Value

For any setting or resetting functionality, a NULL invisibly. For get_env_identifiers a character vector of identifiers for field k. For functions called with no arguments, the entire available identifier list is returned.

list or charvec depends on unify param

list or charvec depends on unify param

NULL

NULL

Details

Identifiers supported by the gDR suite include:

  • "barcode": String of column name containing barcode metadata

  • "cellline": String of column name containing unique, machine-readable cell line identifiers

  • "cellline_name": String of column name containing human-friendly cell line names

  • "cellline_tissue": String of column name containing metadata on cell line tissue type

  • "cellline_ref_div_time": String of column name containing reference division time for cell lines

  • "cellline_parental_identifier": String of column name containing unique, machine-readable parental cell line identifiers. Used in the case of derived or engineered cell lines.

  • "drug": String of column name containing unique, machine-readable drug identifiers

  • "drug_name": String of column name containing human-friendly drug names

  • "drug_moa": String of column name containing metadata for drug mode of action

  • "duration": String of column name containing metadata on duration that cells were treated (in hours)

  • "template": String of column name containing template metadata

  • "untreated_tag": Character vector of entries that identify control, untreated wells

  • "well_position": Character vector of column names containing metadata on well positions on a plate

Examples

get_env_identifiers("duration") # "Duration"
#> [1] "Duration"