/MalariaTravellers

Primary LanguageR

R code repository for

Systems analysis shows a role of cytophilic antibodies in shaping innate tolerance to malaria

Lautenbach et al. Cell Reports 2022

A systems immunology analysis on natural malaria sheds light on disease tolerance mechanisms associated with cytophilic antibodies and gamma delta T cell expansion.

Table of contents

Repo description

This repository contains R code that was used for analysis and visualization.

This project used multiple omics data:

  • Plasma protein expression (Olink - NPX values)
  • Cell counts (Facs - White blood cell count normalized abundance)
  • IgG subclass response (Cumulative response score based on data from Yman et al. 2019)

Omics Integration

MEFISTO

MEFISTO is a Method for the Functional Integration of Spatial and Temporal Omics data and was used in this study in order to deconvolute the main sources of variation along the temporal axis of time after symptom onset for Plasma protein and cell abundance data mentioned above.

For more information, please read: Velten et al. 2020

MEFISTO is part of the MultiOmicsFactorAnalysis (MOFA), publicly accessible here: MEFISTO

  • scripts/MEFISTO.R Script used to train MEFISTO model

Figures

R markdown scripts to reproduce Figures

  • scripts/Figure1.Rmd used for Figure 1B, D-E
  • scripts/MEFISTO_downstream.Rmd used for Figures 2 & 4A,C & S2A-C & S4B
  • scripts/InternalExternalComparison.Rmd used for Figures S1C-D & S2D-G & S3
  • scripts/Correlation.Rmd used for Figures 3 & 4B & 7B-E
  • scripts/CRScore_calculation.Rmd used for Figure S7A-B
  • scripts/Additional_analysis.Rmd used for Figure S4A and S7C-H