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OlinkAnalyze (version 3.8.2)

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

1,906

Version

3.8.2

License

AGPL (>= 3)

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Repository

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

Maintainer

Kathleen Nevola

Last Published

June 27th, 2024

Functions in OlinkAnalyze (3.8.2)

olink_displayPlateLayout

Plot all plates colored by a variable

olink_lmer_plot

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

olink_fill_discrete

Olink fill scale for discrete ggplots

olink_lmer_posthoc

Function which performs a linear mixed model posthoc per protein.

olink_fill_gradient

Olink fill scale for continuous ggplots

olink_dist_plot

Function to plot the NPX distribution by panel

Function which performs a linear mixed model per protein

olink_heatmap_plot

Function to plot a heatmap of the NPX data

olink_normalization_bridge

Bridge normalization of all proteins between two NPX projects.

olink_one_non_parametric_posthoc

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

olink_normalization

Normalization of all proteins (by OlinkID).

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_one_non_parametric

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

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_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_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_pathway_heatmap

Creates a heatmap of selected pathways and proteins

olink_ordinalRegression_posthoc

Function which performs an posthoc test per protein.

olink_pathway_enrichment

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

Olink color panel for plotting

Function which performs a t-test per protein

Function to plot an overview of a sample cohort per Panel

olink_pathway_visualization

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

olink_umap_plot

Function to make a UMAP plot from the data

olink_plate_randomizer

Randomly assign samples to plates

Function to plot a PCA of the data

Helper function to read in Olink Explore csv or txt files

read_npx_parquet

Helper function to read in Olink Explore parquet output files

olink_volcano_plot

Easy volcano plot with Olink theme

Function which performs a Mann-Whitney U Test per protein

Function to read NPX data into long format

Read in flex data

print_and_capture

Capture the output of printing an object

Function to set plot theme

Helper function to read in Olink Explore zip csv files

olink_bridgeselector

Bridge selection function

olink_color_discrete

Olink color scale for discrete ggplots

NPX Data in Long format, Follow-up

check_data_completeness

Check data completeness

Function which plots boxplots of selected variables

olink_color_gradient

Olink color scale for continuous ggplots

olink_anova_posthoc

Function which performs an ANOVA posthoc test per protein.

Function which performs an ANOVA per protein

Calculate LOD using Negative Controls or Fixed LOD

Example Sample Manifest

NPX Data in Long format

olink_displayPlateDistributions

Plot distributions of a given variable for all plates