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pre_bayMeth.R

+# Packeges --------
+library("dplyr")
+library("Repitools")
+library("stringr")
+library("purrr")
+library(rtracklayer)
+library("BSgenome.Sscrofa.ENSEMBL.susScr11")
+
+#windows genome
+windows <- genomeBlocks(Sscrofa, width=100, spacing=100)
+# CPG density files
+cpgDens <- cpgDensityCalc(windows, organism=Sscrofa, w.function="linear", window=500)
+
+
+# saveRDS(windows, file = "/work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS")
+# save(cpgDens, file = "/work2/genphyse/genepi/guillaume/rosepigs/cpgDens.RData")
+
+# windows_genome <- readRDS("/work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS")
+# load("/work2/genphyse/genepi/guillaume/rosepigs/cpgDens.RData")
+
+methyl1 <- readRDS("/work2/genphyse/genepi/guillaume/rosepigs/annotationBlockCountRDS/Tem-methyl_R1.rds")
+methyl2 <- readRDS("/work2/genphyse/genepi/guillaume/rosepigs/annotationBlockCountRDS/Tem-methyl_R2.rds")
+methyl3 <- readRDS("/work2/genphyse/genepi/guillaume/rosepigs/annotationBlockCountRDS/Tem-methyl_R3.rds")
+methyl4 <- readRDS("/work2/genphyse/genepi/guillaume/rosepigs/annotationBlockCountRDS/Tem-methyl_R4.rds")
+
+
+control_minus <- matrix(c(methyl1, methyl2), ncol  = 2)
+control_plus <- matrix(c(methyl3, methyl4), ncol  = 2)
+
+controls_p <- matrix(rowSums(control_plus))
+controls_m <- matrix(rowSums(control_minus))
+
+saveRDS(controls_p, file = "/work2/genphyse/genepi/guillaume/rosepigs/control_plus.rds")
+saveRDS(controls_m, file = "/work2/genphyse/genepi/guillaume/rosepigs/control_minus.rds")
+
+