Update qqPlot.R

analysisScripts/qqPlot.R

@@ -3,26 +3,43 @@ head(hladrData)
 
 hladr_si <- hladrData[, c(1,2,4,6,8,10)]
 hladr_bal <- hladrData[, c(1,3,5,7,9,11)]
+
 # avarge si and bal data
 hladr_si$avg <- (hladr_si$B1_SPU_HLDADR+hladr_si$B2_SPU_HLDADR + hladr_si$B3_SPU_HLDADR + 
                    hladr_si$B4_SPU_HLDADR + hladr_si$B5_SPU_HLDADR)/5
 head(hladr_si)
 hladr_bal$avg <- (hladr_bal$B1_LAV_HLDADR+hladr_bal$B2_LAV_HLDADR + hladr_bal$B3_LAV_HLDADR + 
                     hladr_bal$B4_LAV_HLDADR + hladr_bal$B5_LAV_HLDADR)/5
 head(hladr_bal)
+
+# subgroup only cell specific CpGs
+cpgs <- read.table("cellSpecificCpGs.txt", stringsAsFactors = F, header = T)
+hladr_cpgs <- merge(cpgs, hladr_bal, by = "ProbeID")
+head(hladr_cpgs)
+hladrCpGs <- hladr_cpgs[,c(8,2)]
+head(hladrCpGs)
+colnames(hladrCpGs)[2] <- "type"
 # Create a second file for MWW test
 hladr_siAVG <- hladr_si[,c(1,7)]
 hladr_siAVG$type <- rep("SI")
 head(hladr_siAVG)
 hladr_balAVG <- hladr_bal[,c(1,7)]
-hladr_balAVG$type <- rep("BAL")
+hladr_balAVG$type <- rep("orig")
 head(hladr_balAVG)
-
+dim(hladr_balAVG)
+allHLADRbal <- hladr_balAVG[,c(2,3)]
+head(allHLADRbal)
+## Create data for qqplot
+qqhladr <- rbind(allHLADRbal, hladrCpGs)
+qqPlot(qqhladr$avg)
 
 qqnorm(hladr_balAVG$avg, pch = 1, frame = FALSE)
 qqline(hladr_balAVG$avg, col = "steelblue", lwd = 2)
 
 
 library("car")
-qqPlot(hladr_balAVG$avg)
+qqData <- hladr_cpgs[,c(2, 8)]
+qqPlot(qqData$avg)
+
+qqPlot(hladr_cpgs$avg)
 qqPlot(hladr_siAVG$avg)