Convert cytokine combination format to or from COMPASS format — convert_cyt_combn

Convert cytokine combination format between COMPASS format and "standard " +/- format. See cyt_combn parameter for details. NOTE: At present only converts from COMPASS to standard format.

Usage

convert_cyt_combn_format(
  cyt_combn,
  to,
  force = FALSE,
  silent = FALSE,
  check = TRUE,
  lab = NULL
)

Arguments

cyt_combn: character vector. Cytokine combination, specified either in "<cyt><+-><cyt><+-><cyt><+->..." (e.g. IFNg+IL2-TNF+) or COMPASS "<!><cyt>&<!><cyt>&<!><cyt>..." (e.g. IFNg&!IL2&TNF) format.
to: 'compass' or 'std'. Format to convert to. If 'compass', then output format is COMPASS format (specified above). If 'std', then output format is standard format (specified above).
force: logical. If TRUE, then the code to convert to the specified format will be run. If FALSE, then checks are made to ensure that conversion is not done if already in the requested format. Default is FALSE.
silent: logical. If FALSE, then warnings are printed if force == FALSE and it is detected that cyt_combn already appears to be in the requested format. Default is FALSE.
check: logical. If TRUE, then the converted format is checked that each element has the same number of cytokines. Note that check is only performed if the conversion is attempted. Default is TRUE.
lab: named character vector. Names are names for markers/channels as found in the cytokine combination, and elements are corresponding names/channels. If NULL, then no labelling is done. Default is NULL.

Value

character vector.

Examples

convert_cyt_combn_format(c("IFNg&!IL2"), to = "std")
#> [1] "IFNg+IL2-"
convert_cyt_combn_format(c("IFNg+IL2-"), to = "compass")
#> [1] "IFNg&!IL2"