Create PC_regression_analysis_plots.R

V-Catherine · Jun 10, 2020 · 258dabe · 258dabe
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commit 258dabe
Showing 1 changed file with 17 additions and 0 deletions.
diff --git a/PC_regression_analysis_plots.R b/PC_regression_analysis_plots.R
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+################
+# Principal component regression analysis plots
+###############
+# select variables of interest
+head(pData(fun_filtered))
+pData2 <- data.frame(pData(fun_filtered))
+pData2$sentrix_id = as.factor(pData2$sentrix_id)
+
+lev = apply(pData2,2,function(x) table(x))
+pData2 = pData2[,(sapply(lev,max,na.rm=T)>1)&(sapply(lev,nrow)>1) ]
+
+#svg("PCA.svg",h=6,w=6)
+pcrplot(minfi::getBeta(fun_filtered), cov= pData2, npc=20)
+#dev.off()
+
+# write session info
+writeLines(capture.output(sessionInfo()), "sessionInfo.txt")