Up: Component summary
Up: Component summary
Component
DSRTplotsPlots the inhibition curves for each screening experiments, combine plots for different pretreatment times and computes the scores indicating the efficacy of each drug.
| Version | 1.0 |
|---|---|
| Bundle | dsrt |
| Categories | Preprocessing Excel |
| Authors | Chiara Facciotto (chiara.facciotto@helsinki.fi) |
| Requires | R ; xlsx (R-package) |
| Source files | component.xml DSRTplots.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | CSV | Mandatory | Array of CSV with the measurements from each plate. |
| annotations | CSV | Mandatory | File containing all drugs used in the experiment and the classes they belong to. |
Outputs| Name | Type | Description |
|---|---|---|
| out | Array<CSV> | Array of CSV containg the list of drugs and the related scores used to evaluate the efficacy of each drug |
| normalized | Array<CSV> | Array of CSV with the normalized measurements from each plate. |
| plots | BinaryFolder | Folder containing inhibition plots. |
| combined | BinaryFolder | Folder containing inhibition plots of all pretreatment times. |
| scores | BinaryFolder | Folder containing bar plots representing the absolute score of each drug. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| activityThr | int | 20 | Minimium inhibition that a drug needs to reach in order to be considered active. |
| combine | boolean | true | Parameter indicating whether or not to combine all curves into one single plot |
| neg | string | "DMSO" | Name of the negative control. |
| pos | string | "BzCl" | Name of the positive control. |