Functions package providing manipulation and application of the DoOR.
Details
| Package: | DoOR.functions |
| Type: | Package |
| Version: | 2.0.0 |
| Date: | 2016-01-25 |
| License: | GPL-3 |
| LazyLoad: | yes |
Type help(package = DoOR.functions) to see a complete list of
datasets and functions. Below is what you need for a quick start.
First, load the DoOR packages, data and function package:
library(DoOR.functions): | |
library(DoOR.data): |
then, load all datasets including the precomputed response matrix:
load_door_data: | Load all data into current active environment (function comes with DoOR.data) . |
or, load all odorant reseponse data into a list:
load2list: | Load odorant response data only and compose them as a list. |
Try some visualizations (e.g. producing the plots from the paper):
dplot_al_map: | response to a chemical mapped onto an image of the antennal lobe. |
dplot_compare_profiles: | compare the results of two studies. |
dplot_response_matrix: | Dot Plot of Odorant Responses Across Receptors. |
dplot_response_profile: | bar plot: one receptor, all chemicals. |
dplot_tuningCurve: | pyramid diagram depicting a receptor's tuning breadth. |
Try some queries:
get_responses: | given a chemical, get original responses from all studies in the database. |
get_normalized_responses: | given a chemical, get normalised responses from all studies in the database. |
In case you wish to create your own response model (e.g. because you want to include your own datasets):
create_door_database: | compute the complete response model for all receptors in the database
(calls model_response for all receptors). |
model_response: | run the DoOR algorithm, that merges all measurements for one receptor. |
Estimate odorant responses:
estimate_missing_value: | estimate NA entries in a consensus response data. |
Project the model response values back to tested values:
back_project: | project the model response values back to tested values. |
Introduce new data into DoOR and update the supported data sets:
import_new_data: | import new data into DoOR, and update the weight, response range and receptor names. |
update_door_database: | update response matrix by calculating new consensus response data for a given receptor. |
See the Vignettes and the help pages for more documentation.