This function processes multiple contrasts, performs an analysis, and returns a data frame with the results.
Key features include:
Multiple contrast processing: Ability to process and analyze multiple contrasts.
Comprehensive Analysis: Performs a range of analyses based on user preferences, including Likelihood Ratio, empirical p-value, area under the curve (AUC) for both condition and control, maximum growth rate of the condition, maximum difference, and maximum optical density (OD) for both condition and control.
Output and Display Formats: Provides an option to save results to a TSV file.
Usage
multiple_comparisons(
object,
comparison_list,
predict_n_steps = 50,
downsample_every_n_timepoints = 1,
permutation_test = FALSE,
n_permutations = NULL,
n_cores = 1,
write_to_tsv = FALSE,
save_perm_stats = FALSE,
filename = NULL
)Arguments
- object
DGrowthR object that has been instantiated.
- comparison_list
A list of of vectors. Each vector contains the information for an individual contrast.
- predict_n_steps
A numeric value specifying the number of time points for prediction. Defaults to 50.
- downsample_every_n_timepoints
A numeric value that indicates how timepoints are sampled to increase fit speed
- permutation_test
A logical value indicating if a permutation test should be performed.
- n_permutations
Number of permutations for the permutation test (default: 100).
- n_cores
Number of cores to use for the permutation test (default: 1).
- write_to_tsv
A logical value inndicating if the results should be save to a tsv file.
- save_perm_stats
A logical value indicating whether the permuted test statistics should be stored in the DGrowthR object.
- filename
Name of the TSV file.