RankDysTF: Rank TF with dysregulatin degree

In SCBIT-YYLab/DysRegSig: Gene dysregulation analysis and construction of mechanistic signature in cancer

Description

Rank TF based on dysregulation degree quantified by combining differential regulation and differential expression.

Usage

RankDysTF(dysreg)

Arguments

dysreg

The results of DysReg.

Value

The rank of TFs.

See Also

RankDysReg

Examples

data(ExpData)
data(tf2tar)
data(ClinData)

group.1 <- ClinData$sample[which(ClinData$binaryResponse == 'CR/PR')]
exp.1 <- ExpData[,colnames(ExpData) %in% group.1]

group.2 <- ClinData$sample[which(ClinData$binaryResponse == 'SD/PD')]
exp.2 <- ExpData[,colnames(ExpData) %in% group.2]


dysreg.out <- DysReg(exp.1 = exp.1, exp.2 = exp.2, tf2tar, 
                     de.genes = NULL, de.pval = 0.05, 
                     grn.method = 'Boruta', 
                     pValue = 0.01, ci = 0.90, verbose = T)

dysreg.res <- dysreg.out$dysreg

tf.rank <- RankDysTF(dysreg = dysreg.res)
head(tf.rank)

SCBIT-YYLab/DysRegSig documentation built on July 19, 2021, 4:38 a.m.