Man pages for OlinkAnalyze
Facilitate Analysis of Proteomic Data from Olink
| check_data_completeness | Check data completeness |
| manifest | Example Sample Manifest |
| mapping_file_id | Identifying which mapping file to use |
| 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... |
| norm_internal_assay_median | Compute median value of the quantification method for each... |
| norm_internal_bridge | Internal bridge normalization function |
| norm_internal_cross_product | Internal function normalizing Olink Explore 3k to Olink... |
| norm_internal_reference_median | Internal reference median normalization function |
| norm_internal_rename_cols | Update column names of non-reference dataset based on those... |
| norm_internal_subset | Internal subset normalization function |
| norm_internal_update_maxlod | Update MaxLOD to the maximum MaxLOD across normalized... |
| 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_bridgeability_plot | Plots for each bridgeable assays between two platforms /... |
| 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... |
| 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... |
| olink_lmer_posthoc | Function which performs a linear mixed model posthoc per... |
| 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... |
| olink_normalization_bridgeable | Identify if assays shared between Olink Explore 3072 and... |
| olink_normalization_n | Bridge and/or subset normalization of all proteins among... |
| olink_normalization_n_check | An internal function to perform checks on the input of the... |
| olink_normalization_product_format | Formatting the output of olink_normalization_product for... |
| olink_normalization_project_name_check | An internal function to perform checks on the input project... |
| olink_normalization_qs | Quantile smoothing normalization of all proteins between two... |
| olink_normalization_sample_check | An internal function to perform checks on the input samples... |
| olink_normalization_subset | Subset normalization of all proteins between two NPX... |
| olink_norm_input_assay_overlap | Check datasets and reference_medians for Olink identifiers... |
| 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... |
| 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... |
| olink_norm_input_ref_medians | Check datasets of reference_medians |
| olink_norm_input_validate | Validate inputs of normalization function |
| olink_norm_product_id | Identify names of product for each project |
| olink_norm_reference_id | Identify reference project. |
| olink_one_non_parametric | Function which performs a Kruskal-Wallis Test or Friedman... |
| olink_one_non_parametric_posthoc | Function which performs posthoc test per protein for the... |
| olink_ordinalRegression | Function which A two-way ordinal analysis of variance can... |
| 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... |
| olink_pathway_heatmap | Creates a heatmap of selected pathways and proteins |
| olink_pathway_visualization | Creates bargraph of top/selected enrichment terms from GSEA... |
| 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 |
| pipe | Pipe operator |
| 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 |
