Man pages for skimlab/CCSBUtils
R Utilitiy Functions for CCSB
| classification_summary_workflow | Workflow to get all classification performance |
| combine_batches | Combine SummarizedExperiment objects and correct batch effect |
| combine_batches_dfs | Combine SummarizedExperiment objects and correct batch effect |
| combine.predicted.list | combine outcomes of multiple predictors |
| compute_difference | A function to compute difference between two classes |
| compute_pca | A function to perform *PCA* projection of data |
| compute_tsne | A function to perform *t-SNE* projection of data |
| compute_umap | A function to perform *UMAP* projection of data |
| construct_feature_heatmaps | An internal function to construct heatmaps from feature maps |
| construct_feature_maps | Extract all performance metrics |
| counts_to_cpm | Convert counts to counts per million (CPM). |
| counts_to_tpm | Convert counts to transcripts per million (TPM). |
| cv_loop_train | iterates training a model with CV (serial version) |
| cv_loop_train_iter | A function to train a model with CV |
| cv_loop_train_parallel | iterates training a model with CV (parallel version), using... |
| cv_train_final | A function to train a *final* model with CV |
| extract_metrics | Extract performance metrics from 'performance_summary' slot |
| feature_boxplots | A function to construct boxplots for selected features |
| filter_features | A function for filtering-based feature selection, using... |
| filter_features_AUC | A function for filtering-based feature selection, using... |
| flatten.predict.multiclass | flatten the outcomes of 'multilayer.predict.type' |
| flatten.predict.multilayer | flatten the outcomes of 'multilayer.predict.type' |
| get_selected_features | A function to get selected features from a model, 'fit' |
| get.subsamples | get subset of samples with 'predicted' = 'cls' |
| ggplot_train_trajectory | Create line plots to show train trajectories |
| gtf_to_gene_length | A function to extract 'gene_length' from GTF data frame |
| heatmap_features_cor | Create a heatmap of correlation between features (rows) |
| heatmap_glmnet | Create a heatmap of projected data (coef x data) with... |
| heatmap_prediction | Create a heatmap of data with predicted outcomes at the top... |
| models_performance_summary | Generate a summary of performance of CV trained models |
| mult_wilcox_test | Internal function for multiple Wilcox test |
| plot_projection | A function to visualize/plot a projection |
| predict.consensus | apply a list of models to a set of samples |
| predict.consensus.multiclass | apply a list of models to a set of samples |
| predict.consensus.subclass | sub-classify a subset of samples belonging to a class |
| predict.consensus.type | convert the outcomes of 'predict.consensus' to the one... |
| prediction_consensus_summary | Generate a consensus summary of outcomes |
| prediction_summary | Generate a list of prediction summary |
| prediction_tables | predict outcomes of observations in data using *selected... |
| predict.multiClass | apply a list of models to a set of samples |
| predict.multilayer | predict outcomes of observations in data using *selected... |
| predict.type | predict outcomes of observations in data using *selected... |
| predict.type.multiclass | apply a list of models to a set of samples |
| predict.type.subclass | sub-classify a subset of samples belonging to a class |
| quantize_robust_zscore | Quantize values in a matrix |
| read_gmt | A function to read GMT file |
| robust_zscore | Compute Robust Z score |
| save.PDF.Heatmap | A function to save a Heatmap object to a PDF file |
| size.Heatmap | A function to estimate the drawing size of Heatmap object |
| split_se | Split SummarizedExperiment object |
| train_cv_model_glmnet | A function train a model with CV |
| train_to_final_model | A function that combines cv_loop_train and cv_train_final |
