ab_panel_to_fcs: Write antibody related information into a fcs file

In Close-your-eyes/fcexpr: Complement the manual analysis of flow cytometric experiments and organize your fcs files in a consistent way

Write antibody related information into a fcs file

Description

This writes channel descriptions and optional keywords to fcs files.

Usage

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(),
  clear_previous = F,
  ignore_duplicate_ag = F,
  machine = NULL,
  manual_df = NULL
)

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?
ignore_duplicate_ag	whether or not to ignore duplicate antigen entries in antibody calculation sheet
machine	name of the Flow Cytometer the FCS were acquired on. Only necessary when channels cannot be matched unambiguously.
manual_df	manually provide a data frame with AbCalcFile_col, AbCalcSheet_col and FilePath columns for every FCS file to write channel information to; sampledescription, FileNames, FCS.file.folder are not required when !is.null(manual_df)

Value

no return, but updated fcs files on disk

Examples

## Not run: 
fcexpr::ab_panel_to_fcs(sampledescription = sd,
FileNames = sd$FileName,
FCS.file.folder = file.path(wd, "FCS_files"),
other_keywords = c("Isotype", "Clone", "totalDF", "Vendor", "Cat", "Lot"))

## End(Not run)

Close-your-eyes/fcexpr documentation built on Sept. 29, 2023, 12:27 a.m.