This package, cosinoRmixedeffects2, is forked from cosinoRmixedeffects. cosinoRmixedeffects makes an excellent implementation of mixed effects model to calculate the effect size, confidence intervals, standard errors and p-values using a bootstrapping approach while comparing the rhythmicity parameters MESOR, amplitude and acrophase across two or more groups. In the circadian bioinformatics, this approach is called as differential rhythmicity as it compares the rhythmicity between 2 or more groups.
Prior to the differential rhythmicity analysis, a pre-filtering step is required to check whether at least one of the groups show rhythmicity in the measured entity such as gene expression. For example, let's assume that we would like to test the differential rhythmicity of 3 genes (gene_1, gene_2, gene_3) between 2 groups (group_A, group_B). Below ✓ and ✕ shows if a gene is rhythmic or not rhythmic, respectively.
| Gene | group_1 | group_2 |
|---|---|---|
| gene_1 | ✓ | ✓ |
| gene_2 | ✓ | ✕ |
| gene_3 | ✕ | ✕ |
Imagine that you ran a differential rhythmicity analysis for gene_3 and it turned out to be statistically significant. However, remember that gene_3 did not show any rhytmicity neither in group_1 nor in group_2. This will obviously lead to a false positive discovery. Therefore, genes (or whatever feature you are testing) that do not show any rhythmicity should be discarded from differential rhythmicity analysis. In the toy example above, we should keep gene_1 and gene_2 while filtering out gene_3 for differential rhythmicity analysis.
cosinoRmixedeffects2 can perform rhythmicity analysis while keeping the same methodological principles presented in cosinoRmixedeffects for differential rhythmicity analysis.
Please install devtools if you haven't yet.
install.packages("devtools")
Then, you finally install the cosinoRmixedeffects2 package by using the command below. Warning: It will take some time to build the vignettes, therefore sit back and relax (time for a coffee).
library(devtools)
install_github("altintasali/cosinoRmixedeffects2", build_vignettes = TRUE, dependencies = TRUE)
If you are in a hurry and you know what to do, you can install the package without building the vignettes:
library(devtools)
install_github("altintasali/cosinoRmixedeffects2")
I recommend going through the vignette Rhythmicity and differential rhythmicity analysis for a quick start.
vignette("Rhythmicity_Analysis", package = "cosinoRmixedeffects2")
New features
- Rhythmicity analysis
- Improved acrophase calculation
- New parameter
seed: random seed assignment for reproducible results - CRAN style R package
Bug fixes (from cosinoRmixedeffects)
- Amplitude calculation
- Small improvements and fixes on function parameters