Age-Associated Alterations in T-Cell Proliferation Among Virally Suppressed People With HIV: Processed Data and R Analysis Scripts

This repository contains processed mass cytometry data and R analysis scripts supporting a study of age-associated alterations in T-cell proliferation among people with HIV receiving antiretroviral therapy (ART) with sustained viral suppression. The study included 90 participants, divided into two age groups: younger than 35 years (n = 45) and 35 years or older (n = 45). CD4⁺ and CD8⁺ T-cell populations were analyzed using 20-cluster and 15-cluster classifications, respectively, to investigate age-associated differences in T-cell phenotypes, proliferation, and their associations with inflammatory mediators. Data Files The repository includes four processed datasets: CD4_cluster_frequencies.csv: Participant-level frequencies of 20 CD4⁺ T-cell clusters. CD8_cluster_frequencies.csv: Participant-level frequencies of 15 CD8⁺ T-cell clusters. marker_expression.csv: Marker expression summaries for CD4⁺ and CD8⁺ T-cell clusters, including participant-level and pooled cluster-level median expression values. inflammatory_markers.csv: Participant-level measurements of 23 inflammatory mediators used in the correlation analyses. Analysis Scripts Five R scripts are provided: analysis_parameters.R: Analysis parameters, marker definitions, and input/output configuration. common_functions.R: Shared functions for data processing, FlowSOM clustering, visualization, and statistical analysis. CD4_FlowSOM_analysis.R: CD4⁺ T-cell clustering and downstream analysis. CD8_FlowSOM_analysis.R: CD8⁺ T-cell clustering and downstream analysis. run_combined_inflammation.R: Combined inflammatory mediator correlation analysis, including Benjamini–Hochberg correction across 805 cluster–mediator comparisons (20 CD4⁺ clusters × 23 mediators and 15 CD8⁺ clusters × 23 mediators).