probSameFilt {dc3net}

Filter Probes of The Same Gene

Description

probSameFilt takes the mutual information matrix as input and set the mutual information values of same genes to zero. Thus, it eliminates the interactions between the probes of the same gene.

Usage

probSameFilt(mim, genes)

Arguments

mim

A symmetric square mutual information matrix, where the elements (i,j) correspond to the mutual information I(i,j) or I(j,i) between variables i and j.

genes

A vector of gene names

Details

The use of probSameFilt is very important when working on probe level. If this function is not enabled, then the interactions between probes of the same gene, which should not be taken into account, will be included in differential or common network computation. This may result in difnet or commonnet tables which includes same gene interactions e.g. GPR50-GPR50.

Value

probSameFilt returns mutual information matrix that the interaction scores between probes of the same gene is updated to 0.

Author(s)

Gokmen Altay

References

Altay, G. et. al. "Genome-wide differential gene network analysis software and an application in LnCap prostate cancer", bioRxiv, 2017. Altay, G., Asim, M., Markowetz, F., Neal, D.E. (2011) Differential C3NET reveals disease netwokrs of direct physical interactions. BMC Bioinformatics. 12: 296.

See Also

dc3net,

Examples

  data(tumorData)

  data(geneNames)
  
  tumorData <- copula(tumorData) 
      
  tumorData <- makemim(tumorData)

  probSameFilt(tumorData, geneNames)