RankDysReg: Rank gene dysregulatins

Description Usage Arguments Value See Also Examples

View source: R/DysReg_2.2.3.R

Description

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

Usage

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RankDysReg(dysreg)

Arguments

dysreg

The results of DysReg.

Value

The rank of gene dysregulations.

See Also

RankDysTF

Examples

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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

reg.rank <- RankDysReg(dysreg = dysreg.res)
head(reg.rank)

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