inputCaseA {GRmetrics} | R Documentation

## Simulated dose-response assay data (Case A)

### Description

This is an example dataset corresponding to Case A. The data was generated by the python script "generate_data.py" found in the "inst/scripts/" directory. This object is meant to be used as the "inputData" argument for the `GRfit` function when "case" is equal to "A" (the default option). The input data for "Case A" of the `GRfit` function must be in this format with columns named "concentration", "cell_count", "cell_count__ctrl", and "cell_count__time0" as well as columns for other key variables. The columns "cell_line", "agent", "perturbation", "replicate", and "time" are simply examples of these key variables. It is not necessary that your input data frame include these exact column names or the same number of columns.

### Usage

    inputCaseA

### Format

A data frame with 1008 rows and 9 variables:

- cell_line: the cell-line used (MCF10A, MCF7, BT20)

- agent: the drug used (drugA, drugB, drugC, drugD)

- pertubation: an example of another key variable (e.g different media, a co-treatment, etc.) (0, 1)

- replicate: replicate number, (1, 2, 3)

- time: time of assay measured in hours (48, 72)

- concentration: concentration of the perturbagen on which dose-response curves will be evaluated (not log transformed)

- cell_count: the measure of cell number (or a surrogate of cell number) after treatment at the end of the assay

- cell_count__ctrl: the measure of cell number in control (e.g. untreated or DMSO-treated) wells from the same plate at the end of the assay

- cell_count__time0: the measure of cell number in untreated wells grown in parallel until the time of treatment

### Value

An example dataset in the form of "Case A" generated for use with `GRfit`

### Source

/inst/scripts/generate_data.py

[Package GRmetrics version 1.8.1 Index]