The differential rhythmicity analysis is run with a call to this function. To execute this function, the three necessary ingredients are the timeseries data, the experimental design and parameters to choose and tune the method.
Usage
compareRhythms(
data,
exp_design,
lengths = NULL,
method = "mod_sel",
period = 24,
rhythm_fdr = 0.05,
compare_fdr = 0.05,
amp_cutoff = 0.5,
criterion = "bic",
schwarz_wt_cutoff = 0.6,
just_classify = TRUE,
robust = TRUE,
outliers = FALSE,
longitudinal = FALSE
)Arguments
- data
A matrix of log2 expression values (if microarray), expression counts (RNA-seq) or normalized data (see Details).
- exp_design
A data.frame of the experimental design with at least two columns: "time" and "group".
- lengths
A data.frame of average transcript lengths. Only used with methods "deseq" and "edgeR".
- method
The method of analysis. It should be one of "mod_sel" for model selection, "dodr" for analysis using DODR::dodr, "limma" for linear-modeling approach based on limma, "voom" for linear-modeling approach for RNA-Seq using limma::voom, "deseq2" for RNA-seq analysis using DESeq2, "edger" for RNA-seq analysis using edgeR, and "cosinor" for simple cosinor-based analysis both for independent samples and repeated samples.
- period
The period of rhythm being tested (default = 24)
- rhythm_fdr
The false discovery cutoff for finding rhythmic time series (default = 0.05)
- compare_fdr
The false discovery cutoff for the comparison of rhythms (default = 0.05)
- amp_cutoff
The minimum peak-to-trough amplitude in log2 scale considered biologically relevant (default = 0.5)
- criterion
The criterion used for model selection. These can be "aic" or "bic" (default = "bic"). Only used for method = "mod_sel".
- schwarz_wt_cutoff
The conditional probability that the best model is the true model. Genes with a conditional probability smaller than this cutoff are deemed unclassifiable. This is only used for method = "mod_sel". (default = 0.4)
- just_classify
Boolean specifying whether genes must only be classified (TRUE) or if the amplitude and phases of fits should also be returned (FALSE)
- robust
Boolean to turn on robust computation of statistics in different methods (default = TRUE).
- outliers
Boolean specifying if weights must be computed for each sample to account for outliers. Only used by method = "voom".
- longitudinal
Boolean specifying if repeated samples from one experimental unit. Only used by method = "cosinor".
Value
A data.frame with the names of the differentially rhythmic features, the category it is classified under and optionally the rhythm parameters of the features in each group. The differential rhythmicity categories are gain of, loss of, change of, or same rhythms (with respect to the reference/control group).