Add search for hyper and hypo diff methyl sites

src/diff_methyl.R

@@ -133,10 +133,62 @@ if(file.exists(rdata_file)){
 #   hypo_dfarray <- diff_array[diff_array[,contr_names]<0,]
 #   hyper_dfarray <- diff_array[diff_array[,contr_names]>0,]
 #   gene_hypo_hyper <- Reduce(intersect,  list(hypo_dfarray$Gene_ID,hyper_dfarray$Gene_ID))
+#   methyl_hypo_or_hyper <- Reduce(union,  list(hypo_dfarray$ID,hyper_dfarray$ID))
 #   #write.table(gene_hypo_hyper, paste("DiffMethyl/",contr_names,"_hyper_hypo.txt",sep=""))
-#   print(paste(contr_names,length(gene_hypo_hyper),gene_hypo_hyper))
+#   print(paste("Diff methyl for",contr_names," genes with hypo meth sites",length(hypo_dfarray$Gene_ID)))
+#   print(paste("Diff methyl for",contr_names," genes with hyper meth sites",length(hyper_dfarray$Gene_ID)))
+#   print(paste("Diff methyl for",contr_names," genes with hyper and hypo meth sites",length(gene_hypo_hyper)))
+#   if(length(gene_hypo_hyper)>0){
+#     filter_diff_array = diff_array[diff_array$ID %in% methyl_hypo_or_hyper,]
+#     filter_diff_array = filter_diff_array[filter_diff_array$Gene_ID %in% gene_hypo_hyper,]
+#     write.table(filter_diff_array, paste("DiffMethyl/",contr_names,"_diff_hyper_hypo.txt",sep=""), quote=FALSE, row.names = FALSE, col.names = TRUE, sep = "\t")
+#   }
+# }
+# 
+# 
+# 
+# print("Run save_biocond_list")
+# # # # Play with gene lists
+# bioconds <- unique(as.character(target_epi$BioCond))
+# data_to_bioconds <- list()
+# norm_median_epi <- norm_voom_epi
+# for(i in 1:length(bioconds)){
+#   data_biocond <- as.character(target_epi$labels[target_epi$BioCond==bioconds[i] & target_epi$TypeData=="IP"])
+#   data_to_bioconds[[bioconds[i]]] = data_biocond
+#   norm_median_epi[,bioconds[i]] = apply(norm_median_epi[,data_biocond], 1, function(x) median(x))
+# }
+# 
+# norm_median_epi <- norm_median_epi[,bioconds]
+# norm_median_epi$ID <- rownames(norm_median_epi)
+# norm_median_epi <- merge(norm_median_epi, peaks, by.all = "ID")
+# rownames(norm_median_epi) <-norm_median_epi$ID
+# 
+# cut_off = 2
+# for(biocond in bioconds){
+#   hypo_dfarray <- norm_median_epi[norm_median_epi[,biocond] < (-cut_off),]
+#   hyper_dfarray <- norm_median_epi[norm_median_epi[,biocond] > cut_off,]
+#   gene_hypo_hyper <- Reduce(intersect,  list(hypo_dfarray$Gene_ID,hyper_dfarray$Gene_ID))
+#   methyl_hypo_or_hyper <- Reduce(union,  list(hypo_dfarray$ID,hyper_dfarray$ID))
+#   #write.table(gene_hypo_hyper, paste("DiffMethyl/",contr_names,"_hyper_hypo.txt",sep=""))
+#   print(paste(biocond,"genes with methyl sites hypo",length(hypo_dfarray$Gene_ID)))
+#   print(paste(biocond,"genes with methyl sites hyper",length(hyper_dfarray$Gene_ID)))
+#   print(paste(biocond,"gene with methyl sites hyper and hypo",length(gene_hypo_hyper)))
+#   filter_norm_median_epi = norm_median_epi[norm_median_epi$ID %in% methyl_hypo_or_hyper,]
+#   filter_norm_median_epi = filter_norm_median_epi[filter_norm_median_epi$Gene_ID %in% gene_hypo_hyper,]
+#   write.table(filter_norm_median_epi, paste("DiffMethyl/",biocond,"_all_hyper_hypo.txt",sep=""), quote=FALSE, row.names = FALSE, col.names = TRUE, sep = "\t")
+# }
+# 
+# list_peaks <- diff_peaks
+# norm_median_epi_filter <- norm_median_epi[list_peaks,]
+# for(biocond in bioconds){
+#    hypo_dfarray <- norm_median_epi_filter[norm_median_epi_filter[,biocond] < (-cut_off),]
+#    hyper_dfarray <- norm_median_epi_filter[norm_median_epi_filter[,biocond] > cut_off,]
+#    gene_hypo_hyper <- Reduce(intersect,  list(hypo_dfarray$Gene_ID,hyper_dfarray$Gene_ID))
+#    methyl_hypo_or_hyper <- Reduce(union,  list(hypo_dfarray$ID,hyper_dfarray$ID))
+#    print(paste(biocond,"genes with diff methyl sites hypo",length(hypo_dfarray$Gene_ID)))
+#    print(paste(biocond,"genes with diff methyl sites hyper",length(hyper_dfarray$Gene_ID)))
+#    print(paste(biocond,"gene with diff methyl sites hyper and hypo",length(gene_hypo_hyper)))
+#    filter_norm_median_epi = norm_median_epi_filter[norm_median_epi_filter$ID %in% methyl_hypo_or_hyper,]
+#    filter_norm_median_epi = filter_norm_median_epi[filter_norm_median_epi$Gene_ID %in% gene_hypo_hyper,]
+#    write.table(filter_norm_median_epi, paste("DiffMethyl/",biocond,"_Meth_hyper_hypo.txt",sep=""), quote=FALSE, row.names = FALSE, col.names = TRUE, sep = "\t")
 # }
-# hypo_gfconv <- conv_gf[conv_gf$CONV.GF<0,]
-# hyper_gfconv <- conv_gf[conv_gf$CONV.GF>0,]
-# hypo_gfconv$Gene_ID
-