ab_info_to_panel: Complement the antibody panel table with additional...

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

Complement the antibody panel table with additional information from your antibody list

Description

This function matches the antibodies in a panel to those listed in an antibody list. The antibody list may contain additional information like clone or catalog number which are to be added to the panel table for proper annotation of the experiment. The panel_file should be a xlsx-file as found in the Protocols-folder when running fcexpr::new_exp(). Necessary columns in panel_file and antibody_list used for matching are Antigen, Conjugate, Box, Lot. If they do not exist this function cannot be used, yet. Columns added to the panel_file will appear just right to the LiveDeadMarker column. Anything written there will be overwritten.

Usage

ab_info_to_panel(
  panel_file,
  panel_sheet = "Panel",
  antibody_list,
  antibody_list_sheet = 1,
  antibody_list_cols = c("Reactivity", "Isotype", "Clone", "Vendor", "Cat",
    "Expiry.date", "Concentration.ug.ml", "Recomm.dilution")
)

Arguments

panel_file	character, path to the xlsx file in which the antibody panel was calculated
panel_sheet	character, the name of the sheet in the panel_file
antibody_list	character, path to the xlsx file representing the antibody list with additional information for the used antibodies
antibody_list_sheet	character or numeric, the name or index of the sheet in the antibody_list
antibody_list_cols	character vector, which columns from antibody_list to append to the panel_sheet in panel_file

Details

The following typos in Antigen and Conjugate are rescued (matching may still work with the ab list): Space, special characters (e.g. hyphen), case.

Value

No return value, but an appended panel_file written to disk.

Examples

## Not run: 
ab_info_to_panel(panel_file = "my.path/20220202_Exp.part.1.xlsx",
antibody_list = "/Volumes/AG_Hiepe/_AG-HIEPE_Common/Antibody_List/20200705_antibody_list.xlsx")

## End(Not run)

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