Write antibody related information into a fcs file

This writes channel descriptions and optional keywords to fcs files.

ab_panel_to_fcs(
  sampledescription,
  FileNames,
  FCS.file.folder,
  channel_conjugate_match_file = system.file("extdata",
    "channel_conjugate_matches.xlsx", package = "fcexpr"),
  AbCalcFile_col = "AbCalcFile",
  AbCalcSheet_col = "AbCalcSheet",
  AbCalcFile.folder = file.path(dirname(FCS.file.folder), "Protocols"),
  conjugate_to_desc = T,
  other_keywords = c("Isotype", "Clone", "totalDF", "Vendor", "Cat", "Lot", "Antigen",
    "Conjugate"),
  clear_previous = T
)

Arguments

sampledescription

data frame of sampledescription

FileNames

vector of which fcs files to consider

FCS.file.folder

path to the folder containing the fcs files specified in FileNames

channel_conjugate_match_file

path to an xlsx file holding information about fluorochromes matched to channels (better leave as it is for now)

AbCalcFile_col

column name in sampledescription indicating the file containing the antibody panel calculation

AbCalcSheet_col

column name in sampledescription indicating the respective sheet name in AbCalcFile

AbCalcFile.folder

path to the folder containing the AbCalcFile; if NULL then AbCalcFile_col must contain the full, absolute path of AbCalcFile

conjugate_to_desc

alter/update the channel description of fcs files with stained molecule and optionally the fluorochrome

other_keywords

column names in AbCalcSheet of which keywords to write to fcs files

clear_previous

clear all previous entries (channel descriptions and keywords) in fcs files?

Value

no return, but updated fcs files on disk

Examples

if (FALSE) {

}