plotTpcaVolcano {Rtpca} | R Documentation |
Plot TPCA analysis results
plotTpcaVolcano(tpcaObj, alpha = 0.1)
tpcaObj |
a tpcaObj after having performed
a differential analysis, see |
alpha |
significance level / FDR at which null hypothesis should be rejected |
ggplot displaying a volcano plot
library(dplyr) library(Biobase) m1 <- matrix(1:28, ncol = 4) m2 <- matrix(2:25, ncol = 4) m3 <- matrix(c(2:10, 1:19), ncol = 4) rownames(m1) <- 1:7 rownames(m2) <- 3:8 rownames(m3) <- 2:8 mat_list <- list( m1, m2, m3 ) complex_anno <- tibble( protein = c("3", "4", "5", "4", "5", "6", "7"), id = c(rep("1", 3), rep("2", 4)), count = c(rep(3, 3), rep(4, 4))) tpca_result <- runTPCA( mat_list, complexAnno = complex_anno) plotTpcaVolcano(tpca_result)