MASLD omics data analyses

This repository contains data processing and association analyses for the CHRIS NAFLD (MASLD) data resources.

General data analysis

• General data overview and definition of the MASLD phenotypes: nafld_data_overview.Rmd

Data processing/preprocessing

• Preprocessing of the NAFLD/MASLD untargeted metabolomics data set (positive polarity) NAFLD_Prepro_pos.Rmd.
• Normalisation of the NAFLD/MASLD untargeted metabolomics data set (positive polarity) NAFLD_Norm_pos.Rmd.

Association analyses

• Association analysis of scanningswath proteomics, targeted metabolomics and dietary intake for liver steatosis: NAFLD_steatosis_associations.Rmd. This is the current main analysis.
• Investigation of the confounding effect of PDI on the association analysis of scanningswath proteomics and targeted metabolomics for liver steatosis: NAFLD_steatosis_foodindex_influence.Rmd.
• Association analysis of scanningswath proteomics and targeted metabolomics for liver fibrosis: mNAFLD_fibrosis_explore.Rmd
• Association analysis of scanningswath proteomics and targeted metabolomics for MASH: NAFLD_MASH_and_tables.Rmd
• Association analysis of untargeted metabolomics for liver steatosis: NAFLD_metab_untargeted_pos_lm.Rmd

Pathway analysis

• Pathway analysis using Ramp-DB of scanningswath proteomics and targeted metabolomics was performed online, so no script is available.
• Pathway analysis using Mummichog algorithm of untargeted metabolomics for liver steatosis: NAFLD_naab13_mumichog.Rmd

Preliminary analyses

• Preliminary exploratory analysis of the NAFLD CHRIS sub-study scanningswath proteomics data: NAFLD_scanningswath_proteomics_exploratory_analysis.Rmd
• Analysis to identify Scanning SWATH proteins that are related to liver stiffness, FIB4 variable and liver fat: NAFLD_related_proteins.Rmd
• Preliminary exploratory analysis of the NAFLD CHRIS sub-study targeted metabolomics data: NAFLD_metabolomics_exploratory_analysis.Rmd
• Analysis to identify targeted metabolites that are related to liver stiffness, FIB4 variable and liver fat: NAFLD_related_metabolites.Rmd
• Comparison between the NAFLD participants metabolomics and proteomics measurements in the CHRIS baseline and NAFLD CHRIS sub-study: comparison_nafld_baseline_omics.Rmd
• Compilation of the NAFLD CHRIS sub-study untargeted metabolomics data set: nalfd_untargeted_metabolomics_dataset.Rmd

Required packages and setup

The analysis requires a recent version of R (version >= 3.6.0) and a set of R packages that can be installed with the code below.

install.packages("BiocManager")
library(BiocManager)
BiocManager::install(c("BiocStyle",
                       "xcms",
                       "RColorBrewer",
                       "pander",
                       "UpSetR",
                       "pheatmap",
                       "SummarizedExperiment",
                       "MsExperiment",
                       "Spectra",
                       "MetaboCoreUtils",
                       "MsBackendSql",
                       "MsQuality",
                       "writexl",
                       "ProtGenerics",
                       "MsCoreUtils",
                       "MetaboAnnotation"))

install.packages(c("tidyverse",
                   "readxl",
                   "readr",
                   "RSQLite",
                   "rmarkdown",
                   "kableExtra",
                   "magick",
                   "vioplot",
                   "pandoc",
                   "pander",
                   "car",
                   "DT",
                   "ggfortify",
                   "ggplot2",
                   "ggpubr",
                   "reshape2",
                   "plotly",
                   "rgl",
                   "writexl"))

remotes::install_github("EuracBiomedicalResearch/tidyfr")