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OlinkAnalyze (version 4.2.0)

Facilitate Analysis of Proteomic Data from Olink

Description

A collection of functions to facilitate analysis of proteomic data from Olink, primarily NPX data that has been exported from Olink Software. The functions also work on QUANT data from Olink by log- transforming the QUANT data. The functions are focused on reading data, facilitating data wrangling and quality control analysis, performing statistical analysis and generating figures to visualize the results of the statistical analysis. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.

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Install

install.packages('OlinkAnalyze')

Monthly Downloads

1,416

Version

4.2.0

License

AGPL (>= 3)

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Repository

https://olink.com/ https://github.com/Olink-Proteomics/OlinkRPackage

Maintainer

Kathleen Nevola

Last Published

February 24th, 2025

Functions in OlinkAnalyze (4.2.0)

Function which performs an ANOVA per protein

olink_bridgeselector

Bridge selection function

olink_bridgeability_plot

Plots for each bridgeable assays between two platforms / products Author : Amrita Kar

Function which plots boxplots of selected variables

norm_internal_rename_cols

Update column names of non-reference dataset based on those of reference dataset

norm_internal_subset

Internal subset normalization function

olink_dist_plot

Function to plot the NPX distribution by panel

olink_displayPlateLayout

Plot all plates colored by a variable

olink_fill_discrete

Olink fill scale for discrete ggplots

olink_color_gradient

Olink color scale for continuous ggplots

Calculate LOD using Negative Controls or Fixed LOD

olink_norm_input_assay_overlap

Check datasets and reference_medians for Olink identifiers not shared across datasets.

olink_median_iqr_outlier

Compute outliers based on median +/- iqr_sd * IQR

olink_norm_input_check

Check inputs of olink_normalization function.

olink_lmer_plot

Function which performs a point-range plot per protein on a linear mixed model

Compute inter-quartile range (IQR) of multiplied by a fixed value

Function which performs a linear mixed model per protein

olink_displayPlateDistributions

Plot distributions of a given variable for all plates

olink_color_discrete

Olink color scale for discrete ggplots

olink_lmer_posthoc

Function which performs a linear mixed model posthoc per protein.

olink_norm_input_check_df_cols

Check columns of a list of datasets to be normalized.

olink_norm_reference_id

Identify reference project.

olink_normalization

Normalize two Olink datasets

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_fill_gradient

Olink fill scale for continuous ggplots

Compute median of quantified value

olink_norm_input_validate

Validate inputs of normalization function

olink_norm_product_id

Identify names of product for each project

olink_norm_input_cross_product

Check if bridge or cross-platform normalization

olink_norm_input_clean_assays

Check datasets and reference_medians for unexpected Olink identifiers or excluded assays

olink_normalization_product_format

Formatting the output of olink_normalization_product for seamless use with downstream Olink Analyze functions.

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_norm_input_check_samples

Check reference samples to be used for normalization

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_norm_input_class

Check classes of input in olink_normalization function

olink_heatmap_plot

Function to plot a heatmap of the NPX data

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_one_non_parametric_posthoc

Function which performs posthoc test per protein for the results from Friedman or Kruskal-Wallis Test.

olink_normalization_subset

Subset normalization of all proteins between two NPX projects.

olink_one_non_parametric

Function which performs a Kruskal-Wallis Test or Friedman Test per protein

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.

Function which performs a t-test per protein

olink_umap_plot

Function to make a UMAP plot from the data

olink_ordinalRegression_posthoc

Function which performs an posthoc test per protein.

Olink color panel for plotting

print_and_capture

Capture the output of printing an object

olink_pathway_visualization

Creates bargraph of top/selected enrichment terms from GSEA or ORA results from olink_pathway_enrichment()

Function to plot a PCA of the data

Function which performs a Mann-Whitney U Test per protein

olink_volcano_plot

Easy volcano plot with Olink theme

Helper function to read in Olink Explore zip csv files

olink_plate_randomizer

Randomly assign samples to plates

Function to plot an overview of a sample cohort per Panel

Function to set plot theme

olink_pathway_enrichment

Performs pathway enrichment using over-representation analysis (ORA) or gene set enrichment analysis (GSEA)

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.

Helper function to read in Olink Explore csv or txt files

olink_pathway_heatmap

Creates a heatmap of selected pathways and proteins

read_npx_parquet

Helper function to read in Olink Explore parquet output files

Read in flex data

Function to read NPX data into long format

norm_internal_assay_median

Compute median value of the quantification method for each Olink assay

mapping_file_id

Identifying which mapping file to use

norm_internal_adjust_not_ref

Add adjustment factors to a dataset

Example Sample Manifest

norm_internal_adjust

Combine reference and non-reference datasets

norm_internal_cross_product

Internal function normalizing Olink Explore 3k to Olink Explore 3072

norm_internal_bridge

Internal bridge normalization function

check_data_completeness

Check data completeness

norm_internal_reference_median

Internal reference median normalization function

norm_internal_adjust_ref

Modify the reference dataset to be combined with the non-reference normalized dataset

olink_anova_posthoc

Function which performs an ANOVA posthoc test per protein.

NPX Data in Long format, Follow-up

NPX Data in Long format

norm_internal_update_maxlod

Update MaxLOD to the maximum MaxLOD across normalized datasets.