metaanalysis

03_metaanalysis_step2.R

@@ -40,6 +40,7 @@ metambd2$sample <- with(metambd2, fcase(
     default = ""
 ))
 
+
 # meta plots ---------------
 
 # 95% confidence interval estimation (1/sqrt(N - 1))
@@ -129,17 +130,48 @@ ggsave("mbd2_metaplot.png", p, width = 8, height = 11)
 
 # meta-analysis --------------
 # following the vignette
+
+metambd2$assay <- ifelse(metambd2$assay == "RNAseq", "RNA-seq", "Microarray")
+metambd2$assay2 <- paste0("KO/KD+", metambd2$assay )
+metambd2[study == "Alvarado2013_OE"]$assay2 <- "OE+Microarray"
+mbd2signif <- metambd2[fc_th == 1 & mbd2_padj <= 0.05, ]$study
 settings.meta(digits = 2, method.tau = "PM")
 
-m_all_lfc125 <- metabin(
-    data = metambd2[fc_th == 1.25, ],
-    event.e = n_up, n.e = n_tot,
-    event.c = n_down, n.c = n_tot,
-    studlab = paste(paper, sample),
-    label.e = "Up-regulation", label.c = "Down-regulation",
-    label.left = "More down-regulations", label.right = "More up-regulations"
+mdd <- lapply(
+    setNames(c(1, 1.25, 1.5, 2), c("fcth1", "fcth1.25", "fcth1.5", "fcth2.00")),
+    function(x) {
+        md <- metambd2[fc_th == x & (study %in% mbd2signif), ]
+        metabin(
+            data = md,
+            event.e = n_up, n.e = n_tot,
+            event.c = n_down, n.c = n_tot,
+            studlab = paste(paper, sample),
+            cluster = md$paper,
+            subgroup = md$assay2, subgroup.name = c(""), sep.subgroup = "",
+            sm = "OR", prediction = T,
+            label.e = "Up-regulation", label.c = "Down-regulation",
+            label.left = "More down-regulations", label.right = "More up-regulations"
+        )
+    }
 )
 
-summary(m_all_lfc125)
 
-forest(m_all_lfc125, prediction = TRUE)
+forest(mdd$fcth1, prediction = FALSE)
+forest(mdd$fcth1.25, prediction = FALSE)
+forest(mdd$fcth1.5, prediction = FALSE)
+forest(mdd$fcth2.00, prediction = FALSE)
+
+forest(
+    metabind(
+        mdd,
+        name = c("H0: FC = 1", "H0: 1/1.25 < FC < 1.25", "H0: 1/1.5 < FC < 1.5", "H0: 1/2 < FC < 2"),
+        outclab = "OE test",
+        common = FALSE,
+        prediction = FALSE
+    ),
+    prediction = FALSE
+)
+
+
+
+