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https://github.com/atpoint/circtools

Functions related to analysis of circadian / circular data in R.

https://github.com/atpoint/circtools

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Repository

Functions related to analysis of circadian / circular data in R.

Basic Info
  • Host: GitHub
  • Owner: ATpoint
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 20.5 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

circtools

CI

A little package with functions related to the analysis of circadian / circular data in R. Note that it is mainly intended for my own work, but others are free to use it if you find it useful.

It includes functions to detect rhythmicity in circadian data using cosinor regression as well as adaptations of basic data analysis functions such as intersection, distance and density calculation but modified to respect the circular / periodic nature of the input data. For details, please see the function help at ?function_name.

Functions:

  • run_cosinor() detects circadian rhythmicity using a cosinor model via the limma framework. It scales efficiently to almost any realistic number of samples and observations.
  • circular_density() calculates densities of a vector of circular/periodic values, such as acrophases, respecting the circular nature of the data, thereby avoiding skewed density estimates at the beginning and end of the data range
  • circular_distance() calculates directional circular distance between two timepoints
  • circular_distance_reference() calculates absolute circular distance between a query and one or many reference timepoints
  • circular_intersect() intersects a timepoint with a time window respecting periodicity of data
  • make_data() simulates circadian data based on a cosinor model with adjustable mesor, amplitude and acrophase
  • make_design() creates a design matrix based on the cosinor model for a provided set of timepoints
  • rad2period() converts acrophase values from radians hours to period hours
  • run_model_selection() classifies circadian data from two conditions into differential categories using a model fitting approach, adopted from the compareRhythms package

Installation

```r

Install Bioconductor

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install()

Install limma and circtools

BiocManager::install(c("limma", "atpoint/circtools")) ```

Owner

  • Name: Alexander Bender (né Toenges)
  • Login: ATpoint
  • Kind: user
  • Location: Germany

Postdoc, working in the context of inflammation and cardiovascular disease. Wannabe cyclist and salsa dancer. Dad. Not in that order.

GitHub Events

Total
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 6
  • Fork event: 1
Last Year
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 6
  • Fork event: 1

Dependencies

.github/workflows/tests.yml actions
  • actions/checkout v2 composite
DESCRIPTION cran
  • limma * imports
  • methods * imports
  • stats * imports
  • ggplot2 * suggests