Description Usage Arguments Value See Also Examples
Rank gene dysregualtions based on dysregulation degree quantified by combining differential regulation and differential expression.
1 | RankDysReg(dysreg)
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dysreg |
The results of |
The rank of gene dysregulations.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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)
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