genetic_disease_explore: Explore Gene-Disease Associations

In lharris421/gdexpl: Explore Genes Linked to Diseases and Diseases Linked to Genes

Description

This is a Shiny Gadget that allows the user to easily explore gene associated with certain diseases and vice versa. The user is able to either have a chromoMap built or have a data table produced. The chromoMap has a number of preset diseases that can be explored based on ICD-9 coding. In the future, I plan on expanding the selection possibilities. After the user creates a chromoMap, they will also be able to explore genes and related diseases that appear in the chromoMap. Genes are identified by their geneid which is a Universal number that identifies genes. If the user knows what gene or genes they wish to explore, they may also specify them manually without running a chromoMap. Multiple genes should be seperated by a comma and unreconized genes will produce a connection warning but will not stop the Gadget. In either use case the user may save the necesssary files to reproduce the chromoMap or data table or may have (and specify the name) th object saved to their Global Enviornment upon hitting 'done'. Note, hitting cancel will stop the app and kill any messages but will objects already saved will not be aborted.

Usage

genetic_disease_explore(inputValue1, inputValue2, ...)

Arguments

inputValue1	For shiny gadget
inputValue2	For shiny gadget
...	(optional) The ... take a number of styling options for the chromomap. The options are canvas_height (Numeric), canvas_width (Numeric), chr_color (Character String), anno_col (Character String), chr_width (Numeric), ch_gap (Numeric), labels (T/F).

Details

Directions: Run the function.

1. You can then select a disease and click "Create Chromomap." You may also proceed directly to the gene-disease table where you can specify genes you want to explore if you know their ids. You will also need to select the columns you'd like to use. If this is the case and you have more than one geneid, then seperate others with commas. Click "Create Gene Table

2. After running the chromoMap, you will also be able to select these genes for the disease-gene table. If this is the case make sure you select the map selection.

3. Proceed to chromosome or gene table page. In either page you can output the dataset as a file or to R. If you choose to output to R, you must set an object name - follow proper conventions- or the default will be used.

4. Click 'Done'

Note: Clicking "Cancel" will stop the Gadget and produce and error, but it will not undo already saved files.

Value

A number of different objects or files in and outside of R depending on selections in the gadget. It can return data files, messages, and R objects. Data files for the chromoMap include an annotation file (.txt) and styling file (.rds) Data files for the gene to disease tab can be outputted as a .csv. They can lso be saved to the R global enviornment with a user specified name. The chromomap will be saved as a list, the gene to disease data will be saved as a table. During useage and upon completion, messages will be produced in the console to inform the user of the processes happening on the backend.

Examples

## Not run: 
genetic_disease_explore()

## End(Not run)

lharris421/gdexpl documentation built on Dec. 23, 2019, 6:38 p.m.