README.md

In knifecake/forrelgui: Exclusion Power GUI for the forrel package

forrel - Exclusion Power GUI

Installation

This package requires forrel (available on CRAN) plus some other packages to display the user interface. Installing packages from GitHub requires the package devtools which is available on CRAN and may be installed with

install.packages("devtools")

Once you have devtools you may install forrelgui by pasting the following into an R interactive session:

devtools::install_github("knifecake/forrelgui")

Exclusion power

To launch the exclusion power graphical user interface import the forrelgui package and use the epGUI() function like this:

library("forrelgui")
epGUI()

TODOs

• [x] Load and save projects as .Rdata files
• [x] Load Familias using readFam
• [x] Load and plot pedigrees
• [x] Select individuals available for genotyping
  • [x] Filter IDs so that only those that are possible are shown
• [x] Load and preview frequency databases
  • [x] Set a minimum width for columns
• [x] Load and preview reference profiles
  • [x] Show profile IDs
• [x] Pass a project file to epGUI to open it directly
• [x] Marker settings table
  • [x] Exclude markers from calculation
  • [x] Set mutation models
• [x] Compute EP
  • [x] Show progress during calculation by running one marker at a time
  • [x] Display results in a new tab and focus it
  • [x] Pre-calculation checks
• [ ] Come up with examples for testing
  • [x] Paternity
  • [x] Paternity with reference profiles
  • [x] Familias .fam file with pedigrees and frequency database
  • [ ] A large frequency database
  • [ ] Mutations to showcase mutation models
  • [ ] Examples from the GHEP exercise
  • [ ] Example with Xchrom markers
• [x] Make examples available directly in the program
• [x] Make testing examples loadable to demonstrate the program
• [x] Project settings (file input formats, allele rounding / rogue alleles)
• [ ] Website with help pages?
• [ ] Save report?
• [x] Better About epGUI dialog
• [x] New Project button in the File menu
• [x] Create unrelated pedigree
• [ ] Wrong ID labels in reference table

LICENSE

This project is licensed under the MIT license. See the LICENSE file for details.

knifecake/forrelgui documentation built on March 30, 2021, 10:26 p.m.