read_plates_from_Incucyte_export: Read Incucyte-formatted Excel document for a plate at one or...

In DavidQuigley/HTDoseResponseCurve: Dose Response Curve Evaluation from Incucyte and Other High-Throughput Platforms

Description

read_plates_from_Incucyte_export loads data that have been exported to Excel from the Incucyte platform and returns a data frame of the results, with additional columns for the timestamp, hour, and a user-defined plate identifier. Each call to this function will load the exported values from one or more time points for a single plate map. Individual plate maps can be distinguished in later analysis by the user-provided plate_id parameter.

Usage

read_plates_from_Incucyte_export(path_to_file, plate_id, number_of_wells,
  sheet_num = 1, plate_mask = NA)

Arguments

path_to_file	Path to Excel file generated by the Incucyte software
plate_id	A user-defined string to identify this plate. A plate can be imaged at more than one time point.
number_of_wells	The number of wells per plate, must be 384 or 96
sheet_num	The index of the Excel sheet to read. Defaults to 1.
plate_mask	Indicates which wells to read. Defaults to NA, read all wells. If a matrix of boolean values is passed, read only the wells where plate_mask is TRUE. The matrix must have the same dimensions as the wells being read.

Details

The number of columns will be the columns in the plate plus three additional columns: timestamp, plate_id, and hours. The number of rows will be the number of rows in the plate times the number of plates in the Excel sheet. Excel sheets are read using Hadley Wickham's readxl package.

If the Incucyte instrument only exports a partial plate (e.g. if it does not export every row) this function will including padding for rows and columns that are not in the extract.

Value

A data frame where columns are data, plate_id, hour.

Examples

pkg = "HTDoseResponseCurve"
fn_data_Excel = system.file("extdata", "sample_data_384.xlsx", package = pkg)
plate_data = read_plates_from_Incucyte_export( fn_data_Excel, "p1", 
                                               number_of_wells=384)

DavidQuigley/HTDoseResponseCurve documentation built on Jan. 23, 2021, 5:10 a.m.