plotDysregExp: Visualize expression pattern of a gene dysreglaiton between...

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

Description

Visualize expression pattern of a gene dysreglaiton between conditions.

Usage

plotDysregExp(tf, tar, exp.1, exp.2, 
              exp1.label, exp2.label, 
              method, dysreg, conf.int.level, 
              cor.method = 'pearson', ...)

Arguments

tf	The TF of a gene dysregulation.
tar	The target of a gene dysregulation.
exp.1	Expression matrix of a special condition. Columns correspond to genes, rows correspond to experiments. The matrix is expected to be already normalized.
exp.2	Expression matrix of an another special condition. Columns correspond to genes, rows correspond to experiments. The matrix is expected to be already normalized.
exp1.label	The label condition of exp.1.
exp2.label	The label condition of exp.2.
method	The method of dysregulation analysis, "DysReg", "DiffCor", or "DiffCorPlus".
dysreg	If method is "DysReg", this parameter offers the results of DysReg.
conf.int.level	Level controlling confidence region.
cor.method	Which correlation coefficient (or covariance) is to be computed. One of "pearson" (default) or "spearman", can be abbreviated. the parameter is used while parameter method is "DiffCor", or "DiffCorPlus".
...	Other parameters passed to ggscatter.

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)

dysreg.res <- dysreg.out$dysreg

plotDysregExp(tf = dysreg.res$TF[1], tar = dysreg.res$Target[1],
              exp.1 = exp.1, exp.2 = exp.2, 
              exp1.label = 'Response', exp2.label = 'No-response',
              dysreg = dysreg.res, method ='DysReg', 
              conf.int.level = 0.95)
              

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