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Welcome to the AlveolarCellTypeDeconvolution wiki!
The R scripts to analyze the Alveolar macrophages (HLA-DR+/CD3-) and lymphocytes (CD3+) specific cell types from DNA methylation analysis.
Das, J., Idh, N., Paues, J., Sikkeland, L. I. B., & Lerm, M. (2021). **DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types. \ ** bioRxiv.https://doi.org/10.1101/2021.03.12.435086 \ Epigenetics link
- DNA methylome analysis - till the normalizaed beta value calculation.
- Normality calculation with Anderson's test (Table 1)
- Pearson's rank correaltion analysis - Figures, Table (Figure 2 - a. HLA-DR, b. CD3)
- Beanplot from the beta values of the whole dataset to describe the beta distribution over all samples (Figure S1a)
- Mann-Whitney test for the hypothesis - Figures, Table (Figure 3a - HLA-DR and 3b. CD3)
- Validation of SI and BAL from Lung compartments (Figure 4)
- Testing of 3 reference-free algorithms - algorithms testings, Venn Diagrams (Figure 5a. HLA-DR and Figrue 5b. CD3)
- Cell proportion analysis using the EpiDISH package (Figure 6)
Dockerfile can be used for all R packages and repositories. The image file can be found here
docker pull jd21/alv-decon:latest
| Functions | R scripts | description | notes |
|---|---|---|---|
| ChAMPanalysis450K() | ChAMPanalysis.R | script for DNA methylation using ChAMP | |
| StatiscalAnalysisHLADR() | StatisticalAnalysis.R | ||
| StatiscalAnalysisCD3() | StatisticalAnalysis.R | ||
| ValidationWithCysticFibrosis() | ValidationWithCF.R | ||
| CompareAnalysisRingh() | StatisticalAnalysis.R | ||
| histogramPlot() | Figure2c.R | histogram analysis for beta values | |
| AlveolarCellTypeDeconvolutionRefFreeEWAS() | Figure3.R | Houseman algorithm reference free analysis | |
| AlveolarCellTypeDeconvolutionSVA() | Figure3.R | SVA analysis | |
| AlveolarCellTypeDeconvolutionRefFreeCellMix() | Figure3.R | ||
| AlveolarCellTypeDeconvolutionTOAST() | Figure3.R | ||
| ggplotRegression() | Figure4.R | ||
| sFigure1() | supplementaryFigureS1.R | ||
| sFigure2() | supplementaryFigureS2.R | ||
| qqPlot() | supplementaryFigureS3.R | Q-Q plot for compare DNA methylome data | a sub-function can also be used; gg_qq() |