makeDesign: makeDesign

In AndersenLab/easyXpress: A Package to Read, Process, and Analyze Worm Data Generated from CellProfiler’s WormToolbox

makeDesign

Description

This function will aid in making a design file for an imaging experiment (design.csv).

Usage

makeDesign(
  proj,
  n.plate,
  n.row = 8,
  n.col = 12,
  assay.type = NULL,
  food = NULL,
  od = NULL
)

Arguments

proj	The name of the project this design file will be used for. Remember that the project name always follows the 8-digit date in project directories. For example, the project directory 20200130_toxin01A has a project name of "toxin01A". The project name will be used to join the design file to the cellprofiler-nf output data by the Metadata_Experiment variable, so it is critical that they match exactly.
n.plate	The number of plates in the experiment.
n.row	The number of rows in the plates. Default is 8 for a 96-well plate.
n.col	The number of columns in the plates. Default is 12 for a 96-well plate.
assay.type	OPTIONAL: The type of assay run. For example, "48h".
food	OPTIONAL: A character description of the food used to perform the assay. For example, "15hHB101_20220727".
od	OPTIONAL: The final optical density of bacterial food used in the assay. For example, 10.

Details

The variables output are as follows:

Variables	Class
Metadata_Experiment	chr
Metadata_Plate	chr
Metadata_Well	chr
strain	chr
drug	chr
concentration_um	dbl
bleach	chr
diluent	chr
assay_type	chr
plate	dbl
row	chr
col	chr
food	chr
od	int
well_censor	chr
well_censor_reason	chr
notes	chr

Value

A single data frame with the variables "Metadata_Plate" and "Metadata_Well" variables that can be used as a design file for the readXpress function. The data frame can be augmented further to include specific drugs and dilutents or other experimental design attributes if desired. The variables output include:

AndersenLab/easyXpress documentation built on Dec. 6, 2024, 4:04 a.m.