Alveolar Cell Type Deconvolution

R scripts to analyze the Alveolar macrophages (HLA-DR+/CD3-) and lymphocytes (CD3+) specific cell types from DNA methylation analysis.

Publication:

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. Epigenetics link

BioRxiv. https://doi.org/10.1101/2021.03.12.435086

Create package and R script files according to the analysis (or Result in the manuscript).

1. DNA methylome analysis - till the normalizaed beta value calculation.
2. Normality calculation with Anderson's test (Table 1)
3. Pearson's rank correaltion analysis - Figures, Table (Figure 2 - a. HLA-DR, b. CD3)
4. Beanplot from the beta values of the whole dataset to describe the beta distribution over all samples (Figure S1a)
5. Mann-Whitney test for the hypothesis - Figures, Table (Figure 3a - HLA-DR and 3b. CD3)
6. Validation of SI and BAL from Lung compartments (Figure 4)
7. Testing of 3 reference-free algorithms - algorithms testings, Venn Diagrams (Figure 5a. HLA-DR and Figrue 5b. CD3)
8. Cell proportion analysis using the EpiDISH package (Figure 6)

Use of Docker image

Dockerfile can be used for all R packages and repositories. The image file can be found here

docker pull jd21/alv-decon:latest

Functions present in the package

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()