Man pages for skimlab/CCSBUtils
R Utilitiy Functions for CCSB

classification_summary_workflowWorkflow to get all classification performance
combine_batchesCombine SummarizedExperiment objects and correct batch effect
combine_batches_dfsCombine SummarizedExperiment objects and correct batch effect
combine.predicted.listcombine outcomes of multiple predictors
compute_differenceA function to compute difference between two classes
compute_pcaA function to perform *PCA* projection of data
compute_tsneA function to perform *t-SNE* projection of data
compute_umapA function to perform *UMAP* projection of data
construct_feature_heatmapsAn internal function to construct heatmaps from feature maps
construct_feature_mapsExtract all performance metrics
counts_to_cpmConvert counts to counts per million (CPM).
counts_to_tpmConvert counts to transcripts per million (TPM).
cv_loop_trainiterates training a model with CV (serial version)
cv_loop_train_iterA function to train a model with CV
cv_loop_train_paralleliterates training a model with CV (parallel version), using...
cv_train_finalA function to train a *final* model with CV
extract_metricsExtract performance metrics from 'performance_summary' slot
feature_boxplotsA function to construct boxplots for selected features
filter_featuresA function for filtering-based feature selection, using...
filter_features_AUCA function for filtering-based feature selection, using...
flatten.predict.multiclassflatten the outcomes of 'multilayer.predict.type'
flatten.predict.multilayerflatten the outcomes of 'multilayer.predict.type'
get_selected_featuresA function to get selected features from a model, 'fit'
get.subsamplesget subset of samples with 'predicted' = 'cls'
ggplot_train_trajectoryCreate line plots to show train trajectories
gtf_to_gene_lengthA function to extract 'gene_length' from GTF data frame
heatmap_features_corCreate a heatmap of correlation between features (rows)
heatmap_glmnetCreate a heatmap of projected data (coef x data) with...
heatmap_predictionCreate a heatmap of data with predicted outcomes at the top...
models_performance_summaryGenerate a summary of performance of CV trained models
mult_wilcox_testInternal function for multiple Wilcox test
plot_projectionA function to visualize/plot a projection
predict.consensusapply a list of models to a set of samples
predict.consensus.multiclassapply a list of models to a set of samples
predict.consensus.subclasssub-classify a subset of samples belonging to a class
predict.consensus.typeconvert the outcomes of 'predict.consensus' to the one...
prediction_consensus_summaryGenerate a consensus summary of outcomes
prediction_summaryGenerate a list of prediction summary
prediction_tablespredict outcomes of observations in data using *selected...
predict.multiClassapply a list of models to a set of samples
predict.multilayerpredict outcomes of observations in data using *selected...
predict.typepredict outcomes of observations in data using *selected...
predict.type.multiclassapply a list of models to a set of samples
predict.type.subclasssub-classify a subset of samples belonging to a class
quantize_robust_zscoreQuantize values in a matrix
read_gmtA function to read GMT file
robust_zscoreCompute Robust Z score
save.PDF.HeatmapA function to save a Heatmap object to a PDF file
size.HeatmapA function to estimate the drawing size of Heatmap object
split_seSplit SummarizedExperiment object
train_cv_model_glmnetA function train a model with CV
train_to_final_modelA function that combines cv_loop_train and cv_train_final
skimlab/CCSBUtils documentation built on March 30, 2022, 4:52 a.m.