preprocessMatrices: Remove unnecessary entries from matrices

In DriverNet: Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer

Description

Remove patients (rows) which are not in both matrices from patMutMatrix and patOutMatrix. Remove mutations (columns) from patMutMatrix if they are not a row of influenceGraph. Remove expressions (columns) from patOutMatrix if they are not a column of influenceGraph.

Usage

preprocessMatrices(patMutMatrix, patOutMatrix, influenceGraph)

Arguments

patMutMatrix	Patient Mutation Matrix
patOutMatrix	Patient Outlier Matrix
influenceGraph	Influence Graph Matrix

Value

1	Reduced version of Patient Mutation Matrix
2	Reduced version of Patient Expression(Outlier) Matrix
3	Influence Graph Matrix

Note

The dimension of influenceGraph is not changed.

Author(s)

Ali Bashashati, Reza Haffari, Jiarui Ding, Gavin Ha, Kenneth Liu, Jamie Rosner and Sohrab Shah

Maintainer: Jiarui Ding <[e-mail]>

Examples

data(samplePatientMutationMatrix)
data(samplePatientOutlierMatrix)
data(sampleInfluenceGraph)
tmp = preprocessMatrices(samplePatientMutationMatrix, samplePatientOutlierMatrix, 
sampleInfluenceGraph)

smallerPatientMutationMatrix = tmp[[1]]
smallerPatientOutlierMatrix = tmp[[2]]
influenceGraph = tmp[[3]]

DriverNet documentation built on Nov. 8, 2020, 10:59 p.m.