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.
The outline of the data-analysis steps (presented in DIPP_CyTOF_workflow.R):
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Calculate intensity and proportion tables (batch is IAA, GADA, MULTIPLE separately):
function: DIPP_CyTOF_workflow_intensity_tables_batches function: DIPP_CyTOF_workflow_intensity_tables
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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
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Calculate intensity and proportion tables for celltypes
function: DIPP_CyTOF_workflow_intensity_tables_batches_subclusters function: DIPP_CyTOF_workflow_intensity_tables_batches_subclusters
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Do LME comparisons between Cases and Control for CD4_T and CD8_T
function: DIPP_CyTOF_workflow_lme
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Re-sample tSNE for obtaining publication quality tSNE plot
function: DIPP_CyTOF_workflow_re_tSNE
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Draw plots for the publication
function DIPP_CyTOF_workflow_figures
- 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