# Facilitate Analysis of Proteomic Data from Olink

## Documentation for package ‘OlinkAnalyze’ version 4.5.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

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
norm_internal_update_maxlod | Update MaxLOD to the maximum MaxLOD across normalized datasets.
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 products.
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_format_oid_no_overlap | Retrieve non-overlapping assays between two NPX datasets
olink_format_rm_ext_ctrl | Remove negative controls and plate controls from dataset. For use in olink_normalization_format function. Generates a message stating which control samples were removed.
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_format | Format the output of olink_normalization for seamless use with downstream analysis functions.
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_quant | Check quantification columns.
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_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 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