read_platemap_from_excel: Read plate maps into a list of three data frames

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

Description

A Plate map describes the cell lines, treatment, and treatment concentrations applied to each well. As an alternate to exporting a plate map into XML directly from the instrument, read_platemap_from_excel loads plate map data from an Excel file. The input file must contain cells in column A indicating the values for treatment concentration in uM (e.g. 0.2 for 200 nM), treatment (e.g. the drug in a well), and sample type (e.g. the identifier for a particular cell line in a well). These cells should be one cell up and to the left of plate maps themselves.

Usage

read_platemap_from_excel(filename, sheet_num = 1, number_of_wells,
  concentration_identifier = "concentration",
  treatment_identifier = "treatment", sample_identifier = "cell line",
  na.strings = c("", "NA"))

Arguments

filename	Excel file generated by the user
sheet_num	Index of the Excel sheet to read from filename. Defaults to 1.
number_of_wells	The number of wells in each plate; must be one of 6, 12, 24, 96, 384.
concentration_identifier	Text in a cell in column 1 that signals the concentration map will follow. Defaults to "concentration".
treatment_identifier	text in a cell in column 1 that signals the treatment_identifier map will follow. Defaults to "treatment".
sample_identifier	text in a cell in column 1 that signals the sample_identifier map will follow. Defaults to "cell line".
na.strings	text in a cell that is interpreted as missing data. Defaults to the strings "NA" or an empty cell.

Value

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

Examples

pkg = "HTDoseResponseCurve"
fn_map = system.file("extdata", "sample_data_96_platemap.xlsx",package=pkg)
plate_map = read_platemap_from_excel( fn_map, number_of_wells=96 )

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