DIPP CyTOF

These codes present the dataset specific analysis steps after CyTOF workflow based on following tutorial: https://www.bioconductor.org/help/course-materials/2017/BioC2017/Day2/Workshops/CyTOF/doc/cytofWorkflow_BioC2017workshop.html

In the CyTOF workflow the set cells are clustered by their cell types defined by lineage marker profile. The subsets CD4_T and CD8_T cells where then subsequently divided into subclusters.

DIPP CyTOF data-analysis

The outline of the data-analysis steps (presented in DIPP_CyTOF_workflow.R):

1. Calculate intensity and proportion tables (batch is IAA, GADA, MULTIPLE separately):

   function: DIPP_CyTOF_workflow_intensity_tables_batches function: DIPP_CyTOF_workflow_intensity_tables

2. Do LME comparisons between Cases and Controls

   formula_str <- " ~ Age + Sex + Age*CaseCtrl + (1|Batch) + (1|Pair) + HLA"

   Note: The significance of the sample subsets (IAA-first, GADA-first, ≥2 Aab first groups) was further assessed using the following formula. formula_str <- "~ Age + Sex + HLA + Age*Group + (1|Batch) + (1|Pair)"

   formula_str_per_batch <- " ~ Age + Sex + Age*CaseCtrl + (1|Pair) + HLA"

   function: DIPP_CyTOF_workflow_lme

3. Calculate intensity and proportion tables for celltypes

   function: DIPP_CyTOF_workflow_intensity_tables_batches_subclusters function: DIPP_CyTOF_workflow_intensity_tables_batches_subclusters

4. Do LME comparisons between Cases and Control for CD4_T and CD8_T

   function: DIPP_CyTOF_workflow_lme

5. Re-sample tSNE for obtaining publication quality tSNE plot

   function: DIPP_CyTOF_workflow_re_tSNE

6. Draw plots for the publication

   function DIPP_CyTOF_workflow_figures

System Requirements

• The workflow requires R language version 4.x.
• The workflow has been tested on R 4.1 and 4.3.
• R installation guide: https://cran.r-project.org/doc/manuals/r-release/R-admin.html