check_data_completeness | Check data completeness |
manifest | Example Sample Manifest |
norm_internal_adjust | Combine reference and non-reference datasets |
norm_internal_adjust_not_ref | Add adjustment factors to a dataset |
norm_internal_adjust_ref | Modify the reference dataset to be combined with the non-reference normalized dataset |
norm_internal_assay_median | Compute median value of the quantification method for each Olink assay |
norm_internal_bridge | Internal bridge normalization function |
norm_internal_cross_product | Internal function normalizing Olink Explore 3k to Olink Explore 3072 |
norm_internal_reference_median | Internal reference median normalization function |
norm_internal_rename_cols | Update column names of non-reference dataset based on those of reference dataset |
norm_internal_subset | Internal subset normalization function |
npx_data1 | NPX Data in Long format |
npx_data2 | NPX Data in Long format, Follow-up |
olink_anova | Function which performs an ANOVA per protein |
olink_anova_posthoc | Function which performs an ANOVA posthoc test per protein. |
olink_boxplot | Function which plots boxplots of selected variables |
olink_bridgeselector | Bridge selection function |
olink_color_discrete | Olink color scale for discrete ggplots |
olink_color_gradient | Olink color scale for continuous ggplots |
olink_displayPlateDistributions | Plot distributions of a given variable for all plates |
olink_displayPlateLayout | Plot all plates colored by a variable |
olink_dist_plot | Function to plot the NPX distribution by panel |
olink_fill_discrete | Olink fill scale for discrete ggplots |
olink_fill_gradient | Olink fill scale for continuous ggplots |
olink_heatmap_plot | Function to plot a heatmap of the NPX data |
olink_iqr | Compute inter-quartile range (IQR) of multiplied by a fixed value |
olink_lmer | Function which performs a linear mixed model per protein |
olink_lmer_plot | Function which performs a point-range plot per protein on a linear mixed model |
olink_lmer_posthoc | Function which performs a linear mixed model posthoc per protein. |
olink_lod | Calculate LOD using Negative Controls or Fixed LOD |
olink_median | Compute median of quantified value |
olink_median_iqr_outlier | Compute outliers based on median +/- iqr_sd * IQR |
olink_normalization | Normalize two Olink datasets |
olink_normalization_bridge | Bridge normalization of all proteins between two NPX projects. |
olink_normalization_bridgeable | Identify if assays shared between Olink Explore 3072 and Olink Explore HT can be bridged |
olink_normalization_n | Bridge and/or subset normalization of all proteins among multiple NPX projects. |
olink_normalization_n_check | An internal function to perform checks on the input of the function olink_normalization_n. |
olink_normalization_project_name_check | An internal function to perform checks on the input project names in the functions olink_normalization_bridge and olink_normalization_subset. The function is expected to run all checks on project names to make sure that normalization can be performed smoothly. It should work independently of the function calling it. |
olink_normalization_qs | Quantile smoothing normalization of all proteins between two NPX projects. |
olink_normalization_sample_check | An internal function to perform checks on the input samples in the functions olink_normalization_bridge and olink_normalization_subset. The function is expected to run all checks on SampleID to make sure that normalization can be performed smoothly. It should work independently of the function calling it. |
olink_normalization_subset | Subset normalization of all proteins between two NPX projects. |
olink_norm_input_assay_overlap | Check datasets and reference_medians for Olink identifiers not shared across datasets. |
olink_norm_input_check | Check inputs of 'olink_normalization' function. |
olink_norm_input_check_df_cols | Check columns of a list of datasets to be normalized. |
olink_norm_input_check_samples | Check reference samples to be used for normalization |
olink_norm_input_class | Check classes of input in olink_normalization function |
olink_norm_input_clean_assays | Check datasets and reference_medians for unexpected Olink identifiers or excluded assays |
olink_norm_input_cross_product | Check if bridge or cross-platform normalization |
olink_norm_input_norm_method | Check datasets and reference_medians for Olink identifiers not shared across datasets. |
olink_norm_input_ref_medians | Check datasets of reference_medians |
olink_norm_input_validate | Validate inputs of normalization function |
olink_one_non_parametric | Function which performs a Kruskal-Wallis Test or Friedman Test per protein |
olink_one_non_parametric_posthoc | Function which performs posthoc test per protein for the results from Friedman or Kruskal-Wallis Test. |
olink_ordinalRegression | Function which A two-way ordinal analysis of variance can address an experimental design with two independent variables, each of which is a factor variable. The main effect of each independent variable can be tested, as well as the effect of the interaction of the two factors. |
olink_ordinalRegression_posthoc | Function which performs an posthoc test per protein. |
olink_pal | Olink color panel for plotting |
olink_pathway_enrichment | Performs pathway enrichment using over-representation analysis (ORA) or gene set enrichment analysis (GSEA) |
olink_pathway_heatmap | Creates a heatmap of selected pathways and proteins |
olink_pathway_visualization | Creates bargraph of top/selected enrichment terms from GSEA or ORA results from olink_pathway_enrichment() |
olink_pca_plot | Function to plot a PCA of the data |
olink_plate_randomizer | Randomly assign samples to plates |
olink_qc_plot | Function to plot an overview of a sample cohort per Panel |
olink_ttest | Function which performs a t-test per protein |
olink_umap_plot | Function to make a UMAP plot from the data |
olink_volcano_plot | Easy volcano plot with Olink theme |
olink_wilcox | Function which performs a Mann-Whitney U Test per protein |
print_and_capture | Capture the output of printing an object |
read_flex | Read in flex data |
read_NPX | Function to read NPX data into long format |
read_npx_csv | Helper function to read in Olink Explore csv or txt files |
read_npx_parquet | Helper function to read in Olink Explore parquet output files |
read_npx_zip | Helper function to read in Olink Explore zip csv files |
set_plot_theme | Function to set plot theme |