basis_matrix | Helper methods for the Moanin class |
basis_matrix-method | Helper methods for the Moanin class |
consensus_matrix | Compute consensus matrix from labels |
create_go_term_mapping | Find enriched GO terms |
create_moanin_model | Class Moanin |
create_moanin_model-method | Class Moanin |
create_timepoints_contrasts | Fit weekly differential expression analysis |
create_timepoints_contrasts-method | Fit weekly differential expression analysis |
degrees_of_freedom | Helper methods for the Moanin class |
degrees_of_freedom-method | Helper methods for the Moanin class |
DE_timecourse | Run spline models and test for DE of contrasts. |
DE_timecourse-method | Run spline models and test for DE of contrasts. |
DE_timepoints | Fit weekly differential expression analysis |
DE_timepoints-method | Fit weekly differential expression analysis |
discont_basis | Provides set of basis functions on either side of a time point, allowing for a discontinuity in the fitted functions |
estimate_log_fold_change | Estimates log fold change |
estimate_log_fold_change-method | Estimates log fold change |
exampleData | Small data set for running examples |
find_enriched_go_terms | Find enriched GO terms |
get_auc_similarity_scores | Evaluate the consensus between sets of clusterings |
get_log_data | Helper methods for the Moanin class |
get_log_data-method | Helper methods for the Moanin class |
group_variable | Helper methods for the Moanin class |
group_variable-method | Helper methods for the Moanin class |
group_variable<- | Helper methods for the Moanin class |
group_variable<--method | Helper methods for the Moanin class |
group_variable_name | Helper methods for the Moanin class |
group_variable_name-method | Helper methods for the Moanin class |
group_variable_name<- | Helper methods for the Moanin class |
group_variable_name<--method | Helper methods for the Moanin class |
log_transform | Helper methods for the Moanin class |
log_transform-method | Helper methods for the Moanin class |
Moanin | Class Moanin |
Moanin-class | Class Moanin |
Moanin-methods | Helper methods for the Moanin class |
NULL-method | Rescales rows of data to be between 0 and 1 |
perWeek_barplot | Creates barplot of results of per-timepoint comparison |
plot_cdf_consensus | Evaluate the consensus between sets of clusterings |
plot_model_explorer | Evaluate the consensus between sets of clusterings |
plot_splines_data | Plotting splines |
plot_splines_data-method | Plotting splines |
pvalues_fisher_method | Fisher's method to combine pvalues |
rescale_values | Rescales rows of data to be between 0 and 1 |
rescale_values, | Rescales rows of data to be between 0 and 1 |
rescale_values-method | Rescales rows of data to be between 0 and 1 |
show | Helper methods for the Moanin class |
show-method | Helper methods for the Moanin class |
splines_kmeans | Performs splines clustering using K-means |
splines_kmeans-method | Performs splines clustering using K-means |
splines_kmeans_predict | Assign score and labels from raw data |
splines_kmeans_predict-method | Assign score and labels from raw data |
splines_kmeans_score_and_label | Assign score and labels from raw data |
splines_kmeans_score_and_label-method | Assign score and labels from raw data |
spline_formula | Helper methods for the Moanin class |
spline_formula-method | Helper methods for the Moanin class |
testData | Small data set for running examples |
testGenesGO | Small data set for running examples |
testMeta | Small data set for running examples |
time_by_group_variable | Helper methods for the Moanin class |
time_by_group_variable-method | Helper methods for the Moanin class |
time_variable | Helper methods for the Moanin class |
time_variable-method | Helper methods for the Moanin class |
time_variable<- | Helper methods for the Moanin class |
time_variable<--method | Helper methods for the Moanin class |
time_variable_name | Helper methods for the Moanin class |
time_variable_name-method | Helper methods for the Moanin class |
time_variable_name<- | Helper methods for the Moanin class |
time_variable_name<--method | Helper methods for the Moanin class |
[-method | Helper methods for the Moanin class |