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4 Differential Expression Analysis

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Alireza Khodadadi-Jamayran edited this page Oct 30, 2019 · 1 revision
  • Differential Expression Analysis
diff.res <- run.diff.exp(my.obj, de.by = "clusters", cond.1 = c(1,4), cond.2 = c(2))
diff.res1 <- as.data.frame(diff.res)
diff.res1 <- subset(diff.res1, padj < 0.05)
head(diff.res1)
#             baseMean        1_4           2 foldChange log2FoldChange         pval
#AAK1       0.19554589 0.26338228 0.041792762 0.15867719      -2.655833 8.497012e-33
#ABHD14A    0.09645732 0.12708519 0.027038379 0.21275791      -2.232715 1.151865e-11
#ABHD14B    0.19132829 0.23177944 0.099644572 0.42991118      -1.217889 3.163623e-09
#ABLIM1     0.06901900 0.08749258 0.027148089 0.31029018      -1.688310 1.076382e-06
#AC013264.2 0.07383608 0.10584821 0.001279649 0.01208947      -6.370105 1.291674e-19
#AC092580.4 0.03730859 0.05112053 0.006003441 0.11743700      -3.090041 5.048838e-07
                   padj
#AAK1       1.294690e-28
#ABHD14A    1.708446e-07
#ABHD14B    4.636290e-05
#ABLIM1     1.540087e-02
#AC013264.2 1.950557e-15
#AC092580.4 7.254675e-03

# more examples 
# diff.res <- run.diff.exp(my.obj, de.by = "conditions", cond.1 = c("WT"), cond.2 = c("KO"))
# diff.res <- run.diff.exp(my.obj, de.by = "clusters", cond.1 = c(1,4), cond.2 = c(2))
# diff.res <- run.diff.exp(my.obj, de.by = "clustBase.condComp", cond.1 = c("WT"), cond.2 = c("KO"), base.cond = 1)
# diff.res <- run.diff.exp(my.obj, de.by = "condBase.clustComp", cond.1 = c(1), cond.2 = c(2), base.cond = "WT")
  • Volcano and MA plots
# Volcano Plot 
volcano.ma.plot(diff.res,
	sig.value = "pval",
	sig.line = 0.05,
	plot.type = "volcano",
	interactive = F)

# MA Plot
volcano.ma.plot(diff.res,
	sig.value = "pval",
	sig.line = 0.05,
	plot.type = "ma",
	interactive = F)

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