https://github.com/mayoverse/kinship2

Pedigree creation, plotting, and analytics
https://github.com/mayoverse/kinship2

Last synced: 3 months ago
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Pedigree creation, plotting, and analytics

• Host: GitHub
• URL: https://github.com/mayoverse/kinship2
• Owner: mayoverse
• License: gpl-2.0
• Created: 2017-07-27T15:16:29.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2024-03-08T19:08:24.000Z (4 months ago)
• Last Synced: 2024-03-25T10:12:13.681Z (3 months ago)
• Language: R
• Size: 2.08 MB
• Stars: 11
• Watchers: 5
• Forks: 7
• Open Issues: 18
• Metadata Files:
  • Readme: README.md

Lists

• awesome-r-dataviz - kinship2 - Pedigree creation, plotting, and analytics. [[Vignette]](https://cran.r-project.org/web/packages/kinship2/vignettes/pedigree.html) (ggplot / Domain-specific)

README

        

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# The `kinship2` Package

Initially a set of functions to view pedigrees while developing models that use kinship matrices, the functions were useful enough to put into a package of its own, an S3 class for pedigrees, kinship function that calculates the kinship matrix from a pedigree object, and the pedigree plotting routines that adhere to many of the standards for genetics counselors.

# The `pedigree()` Function

`pedigree()` is a function that creates an S3 class of either one pedigree of a pedigreeList (list of pedigrees), depending on whether the family id is given. The core of the pedigree object is built from having a row per person, linked by the father id and mother id. Other relationships can be specified, and affection status can be a matrix of multiple categories.

# The `plot.pedigree()` Method

`plot.pedigree()` is a method for pedigree a object that plots as a "family tree", with relatives of the same generation on the same row, and affection statuses divided over the plot symbol for each person. 

# The `kinship()` Funtion

`kinship()` is a function that creates the kinship matrix from a pedigree object. It is coded for dyplotype organisms, handling all relationships that can be specified for the pedigree object, including inbreeding, monozygotic twins, etc. A recent addition is handling the kinship matrix for the X and Y chromosomes.  

## Other Notable Functions

* `pedigree.shrink()` will shrink a pedigree to a given size, keeping the most informative individuals for a single affection variable.

* `fixParents()` will add parents for children who have a mother or dad listed that is not already included. It will also fix the sex status for the parent if it is mis-specified.

* legendPlot() is a variation on plot.pedigree, which has an informative legend at the bottom with the ability to put labels for the affection statuses and coloring scheme.