getBM {GeneNT} | R Documentation |
This function takes inputs of screened gene pairs based on BOTH Pearson correlation and Kendall correlation statistics, and generates Pajek compatible Boolean matrix that can be visulized using network visulization software such as Pajek.
getBM(pG2, kG2)
pG2 |
Gene pairs that passed two-stage screening based on Pearson correlation coefficient. |
kG2 |
Gene pairs that passed two-stage screening based on Kendall correlation coefficient. |
A Pajek compatible Boolean matrix "BMPajek.mat" and a R Boolean matrix "BM.tsv" will be exported to the working directory.
"BM.tsv" (R format Boolean matrix) and "BMPajek.mat" (Pajek format Boolean matrix) will be returned.
Dongxiao Zhu (http://dongxiaozhu.googlepages.com/home)
## load GeneNT library library(GeneNT) ## EITHER use the example dataset data(dat) ## Note, data matrix name has to be "dat" ## use (FDR, MAS) criteria (0.2, 0.5) as example to screen gene pairs ## use "BY" procedure to do multiple comparison adjustment g1 <- corfdrci(0.2, 0.5, "BY") pG1 <- g1$pG1 ## pG2 contains gene pairs that passed two-stage screening pG2 <- g1$pG2 g2 <- kendallfdrci(0.2, 0.5, "BY") #use (FDR, MAS) criteria (0.2, 0.5) as example to screen gene pairs kG1 <- g2$kG1 ## kG2 contains gene pairs that passed two-stage screening kG2 <- g2$kG2 ## generate Pajek compatible matrix to visualize network getBM(pG2, kG2)