merge_target_list: Merge Target Gene List for Two Drivers

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Merge Target Gene List for Two Drivers

Description

merge_target_list merges target gene list for two drivers together. Shared target genes with high "MI (mutual information)" statistics will be kept in the final target list.

Usage

merge_target_list(driver1 = NULL, driver2 = NULL, target_list = NULL)

Arguments

driver1	character, the name of the first driver.
driver2	character, the name of the second driver.
target_list	list, the driver-to-target list object. The names of the list elements are drivers (e.g. driver1 and driver2). Each element is a data frame, usually contains at least three columns. "target", target gene names; "MI", mutual information; "spearman", spearman correlation coefficient. Users can call get_net2target_list to create this list.

Value

Return a data.frame with rows of target genes, column of "target", "MI", "spearman".

Examples

analysis.par <- list()
analysis.par$out.dir.DATA <- system.file('demo1','driver/DATA/',package = "NetBID2")
NetBID.loadRData(analysis.par=analysis.par,step='ms-tab')
ms_tab <- analysis.par$final_ms_tab
driver1 <- ms_tab[1,'originalID_label']
driver2 <- ms_tab[2,'originalID_label']
m1 <- merge_target_list(driver1=driver1,driver2=driver2,
                          target_list=analysis.par$merge.network$target_list)

jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.