
Package index
-
hd_initialize()
- Initialize HDAnalyzeR object
-
hd_save_path()
- Create directory to save results
-
hd_save_data()
- Save tibble or R object
-
hd_import_data()
- Import data from file
-
hd_widen_data()
- Convert omics data to wide format
-
hd_long_data()
- Convert omics data to long format
-
hd_bin_columns()
- Bin variables
-
hd_detect_vartype()
- Detect variable type
-
hd_filter_by_sex()
- Filter data and metadata by sex
-
hd_log_transform()
- Log transform data with base 2
Data Normalization and Imputation
Functions that perform normalizaztion, remove batch effects and impute missing values.
-
hd_normalize()
- Normalize data and remove batch effects
-
hd_omit_na()
- Omit missing values
-
hd_impute_median()
- Impute via Median
-
hd_impute_knn()
- Impute via k-nearest neighbors
-
hd_impute_missForest()
- Impute via missForest
-
hd_na_search()
- Heatmap summary of missing values
-
hd_qc_summary()
- Summarize quality control information
Correlation and Clustering
Functions that perform protein-protein correlation and can order data based on selected clustering method.
-
hd_correlate()
- Correlate data
-
hd_plot_cor_heatmap()
- Plot correlation heatmap
-
hd_cluster()
- Cluster data
-
hd_cluster_samples()
- Cluster samples in k clusters
-
hd_assess_clusters()
- Assess clusters
-
hd_pca()
- Run PCA analysis
-
hd_umap()
- Run UMAP analysis
-
hd_plot_dim()
- Plot PCA or UMAP results on a 2D plane
-
hd_plot_pca_loadings()
- Plot PCA loadings
-
hd_plot_pca_variance()
- Plot PCA variance
-
hd_auto_pca()
- Run PCA analysis and plot the results
-
hd_auto_umap()
- Run UMAP analysis and plot the results
Protein Co-expression Network Analysis (WGCNA)
Functions that perform weighted gene co-expression network analysis.
-
hd_wgcna()
- Weighted gene co-expression network analysis
-
hd_plot_wgcna()
- Plot WGCNA results
-
hd_de_limma()
- Differential expression analysis with limma
-
hd_de_ttest()
- Differential expression analysis with t-test
-
hd_plot_volcano()
- Visualize differential expression results
-
hd_split_data()
- Split data
-
hd_model_lr()
- Logistic regression model pipeline
-
hd_model_rreg()
- Regularized regression model pipeline
-
hd_model_rf()
- Random forest model pipeline
-
hd_model_test()
- Validate model on new data
-
hd_plot_de_summary()
- Summarize differential expression results
-
hd_plot_model_summary()
- Summarize model features
-
hd_plot_feature_heatmap()
- Summary the combined DE and model results
-
hd_plot_regression()
- Regression plot
-
hd_plot_feature_boxplot()
- Feature boxplots
-
hd_plot_feature_network()
- Feature network
-
hd_literature_search()
- PubMed literature search
-
hd_ora()
- Over-representation analysis
-
hd_plot_ora()
- Plot over-representation analysis results
-
hd_show_backgrounds()
- Show available background lists
-
hd_gsea()
- Gene set enrichment analysis
-
hd_plot_gsea()
- Plot gene set enrichment analysis results
-
hd_show_palettes()
- Display available palettes
-
hd_palettes()
- HDAnalyzeR palettes
-
scale_color_hd()
- HDAnalyzeR color scales
-
scale_fill_hd()
- HDAnalyzeR fill scales
-
theme_hd()
- HDAnalyzeR theme
-
example_data
- Cancer cohort Olink data
-
example_metadata
- Cancer cohort metadata