Package index • LundTaxR

Package Overview

Package documentation and information

Main functions for molecular subtype classification

Functions for extracting predictions and calculating metrics

Functions for survival analysis and GLM modeling

get_survival(): Cox Model for Calculating Hazard Ratios From Clinical End-points
get_glm(): Get General Linear Model Scores.

Functions for creating plots and heatmaps

plot_classification_heatmap(): Visualize Output from the LundTaxR Classifier in a Heatmap
plot_signatures_heatmap(): Subtype-dependent Visualization of Signature Scores in a Heatmap
plot_ratio_forest(): Visualize Signature Scores (Cox or GLM) in a Forest Plot
plot_subtype_forest(): Subtype Forest Plot
plot_ranked_score(): Plot Ranked Signature Scores in Subtypes
plot_subscore_box(): Visualize Subtype Prediction Scores in a Sorted/ranked/stacked Barplot
plot_subscore_violin(): Visualize Subtype Prediction Scores in A Violin-style plot
get_custom_annotations(): Create Custom Annotation Tracks from Metadata

Built-in datasets and classifier objects

classifier_lundtax_5c: Classifier LundTax 5c.
classifier_lundtax_7c: Classifier LundTax 7c.
classifier_grade_who_1999: SwitchBox Classifier for WHO 1999 Tumor Grading
classifier_grade_who_2022: SwitchBox Classifier for WHO 2022 Tumor Grading
sjodahl_2017: Sjodahl 2017.
sjodahl_2017_meta: Sjodahl 2017 Meta.
gene_list: Gene List.
signatures: Signatures
lund_colors: Lund Colors.
tx2gene: GENCODE v44 Transcript-to-Gene Mapping Table

Internal helper functions (not typically used directly)

int_bin_numeric_variables(): Bin Numeric Variables
int_calc_immune_proportions(): Calculate Immune Proportions.
int_calc_score(): Calculate Immune and Infiltration Scores
int_calc_signatures(): Calculate Lund Taxonomy Signature Scores
int_check_log2_transformation(): Check if RNAseq Expression Data is Log2-Transformed
int_check_ties(): Check Ties Between prediction Scores
int_get_prop_scores(): Get Proportional Signature Scores
int_interpret_score(): Interpret SwitchBox Score
int_merge_suburo_matrix(): Merge Uro Subtype Matrix
int_predict_grade(): Predict Tumor Grade
int_prediction_wrangler(): Prediction Wrangler
int_ratio_score(): Calculate Signature Ratio Scores
create_deprecated_function(): Create Deprecated Function