getBM {GeneNT}R Documentation

Generate Pajek compatible matrix from screened gene pairs

Description

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.

Usage

getBM(pG2, kG2)

Arguments

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.

Details

A Pajek compatible Boolean matrix "BMPajek.mat" and a R Boolean matrix "BM.tsv" will be exported to the working directory.

Value

"BM.tsv" (R format Boolean matrix) and "BMPajek.mat" (Pajek format Boolean matrix) will be returned.

Author(s)

Dongxiao Zhu (http://dongxiaozhu.googlepages.com/home)

See Also

row.names

Examples


## 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) 

[Package GeneNT version 1.4 Index]