test.targetNet.overlap: Test for Intersection of Target Genes between Two Drivers

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

Test for Intersection of Target Genes between Two Drivers

Description

test.targetNet.overlap performs Fisher's exact test to see whether the target genes from two drivers are significantly intersected.

Usage

test.targetNet.overlap(
  source1_label = NULL,
  source2_label = NULL,
  target1 = NULL,
  target2 = NULL,
  total_possible_target = NULL
)

Arguments

source1_label	character, the label of the first selected driver.
source2_label	character, the label of the second selected driver.
target1	a vector of characters, the list of target genes from the first driver.
target2	a vector of characters, the list of target genes from the second driver.
total_possible_target	numeric or a vector of characters. If input is numeric, it is the total number of possible target genes. If input is a vector of characters, it is the background list of all possible target genes.

Value

Return statistics of the testing, including the P.Value, Odds_Ratio and Intersected_Number.

Examples

source1_label <- 'test1'
target1 <- sample(paste0('G',1:1000),size=80)
source2_label <- 'test2'
target2 <- sample(paste0('G',1:1000),size=120)
test.targetNet.overlap(source1_label=source1_label,source2_label=source2_label,
               target1=target1,target2=target2,
               total_possible_target=paste0('G',1:1000))
## Not run: 

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