Update README.md

analyses/methylation_analysis/README.md

@@ -29,7 +29,7 @@ c. gene body + promoter
 ../intNMF/results/intnmf_clusters.tsv
 
 # methylation annotation file
-../../data/v12/infinium.gencode.v39.probe.annotations.tsv.gz
+../../data/v15/infinium.gencode.v39.probe.annotations.tsv.gz
 
 # methylation m-values subsetted to cohort of interest
 ../data_preparation/data
@@ -100,7 +100,7 @@ c. gene body + promoter
 ../intNMF/results/intnmf_clusters.tsv
 
 # methylation annotation file
-../../data/v12/infinium.gencode.v39.probe.annotations.tsv.gz
+../../data/v15/infinium.gencode.v39.probe.annotations.tsv.gz
 
 # methylation m-values subsetted to cohort of interest
 ../data_preparation/data
@@ -137,118 +137,3 @@ plots
         └── promoter_gsaregion_pathways.pdf
 ```
 
-### Differential methylated region analysis (DMRcate) + Pathway Enrichment (fgsea)
-
-`05-dmr_fgsea_analysis.R`: The function of this script is to pull the full medulloblastoma methylation m-values dataset and filter the dataset into probes representing promoter region and gene-body (introns and exons). Next, differential region-level methylation analyses is performed with `DMRcate::dmrcate` using a cluster-of-interest vs 'rest' approach, and specifying 'EPIC' array. Finally, `fgsea::fgsea` analysis is performed on the `genes overlapping` the resulting differentially methylated regions to determine cluster-specific pathway differences. 
-
-Tests of interest:
-a. gene body only
-b. promoter only
-c. gene body + promoter
-
-```
-# intNMF derived clusters
-../intNMF/results/intnmf_clusters.tsv
-
-# methylation annotation file
-../../data/v12/infinium.gencode.v39.probe.annotations.tsv.gz
-
-# methylation m-values subsetted to cohort of interest
-../data_preparation/data
-└── methyl-m-values.rds
-```
-
-TSV file of all significant pathways (`FDR < 0.05`) for each cluster:
-
-```
-results
-└── dmr_fgsea_output
-    ├── hallmark
-    │   ├── gene_body_fgsea_output_per_cluster.tsv
-    │   ├── genebody_promoter_fgsea_output_per_cluster.tsv
-    │   └── promoter_fgsea_output_per_cluster.tsv
-    └── reactome
-        ├── gene_body_fgsea_output_per_cluster.tsv
-        ├── genebody_promoter_fgsea_output_per_cluster.tsv
-        └── promoter_fgsea_output_per_cluster.tsv
-```
-
-Barplots of top 50 pathways (`FDR < 0.05`) enriched in each cluster:
-```
-plots
-└── dmr_fgsea_output
-    ├── hallmark
-    │   ├── gene_body_fgsea_pathways.pdf
-    │   ├── genebody_promoter_fgsea_pathways.pdf
-    │   └── promoter_fgsea_pathways.pdf
-    └── reactome
-        ├── gene_body_fgsea_pathways.pdf
-        ├── genebody_promoter_fgsea_pathways.pdf
-        └── promoter_fgsea_pathways.pdf
-```
-
-### Integration of MethReg output with DIABLO
-
-`06-methreg_diablo_integration.R`: The function of this script is to utilize triplet information from MethReg analysis (i.e. prioritization of differentially methylated CpG sites) and compute an intersection between DIABLO results (with non-zero loadings) and the functional probes that pass the threshold of `RLM_DNAmGroup:TF_fdr` or `RLM_DNAmGroup_fdr` < 0.05. 
-
-#### Inputs
-
-```
-# formatted methylation matrix for MethReg analysis
-results/methreg_output
-└── methylation_matrix_methreg.rds
-
-# formatted expression matrix for MethReg analysis
-results/methreg_output
-└── expression_matrix_methreg.rds
-
-# output of functionally relevant triplets
-results/methreg_output
-└── triplet_nearest_gene_interactions_stratified_model.tsv
-
-# output of DIABLO descriptive analysis
-../diablo/results/intnmf/descriptive
-└── diablo_MB.rds
-```
-
-#### Outputs
-
-```
-# tsv file of triplets intersecting with DIABLO
-results
-└── methreg_output
-    └── diablo_integration
-        └── comp{component_number}_diablo_methreg_intersection.tsv
-
-# interaction model for probes intersecting with DIABLO
-plots
-└── methreg_output
-    └── diablo_integration
-        └── comp{component_number}_diablo_methreg_intersection.pdf
-```
-
-### Integration of Limma output with DIABLO
-
-`06-limma_diablo_integration.R`: The function of this script is to utilize differentially expressed CpG sites obtained from `01-limma_analysis.R` and compute an intersection with DIABLO results (with non-zero loadings).
-
-#### Inputs
-
-```
-# output of differentially expressed CpG sites
-results/limma_output
-└── genebody_promoter_diffexpr_probes_per_cluster.tsv
-
-# output of DIABLO descriptive analysis
-../diablo/results/intnmf/descriptive
-└── diablo_MB.rds
-```
-
-#### Outputs
-
-```
-# tsv file of differential CpGs intersecting with DIABLO
-results
-└── limma_output
-    └── diablo_integration
-        └── comp{component_number}_diablo_limma_intersection.tsv
-```