bioDistW: bioDistW

In llrs/STATegRa: Classes and methods for multi-omics data integration

Description

Function that computes weighted distances between a list of bioDistclass objects.

Usage

bioDistW(referenceFeatures, bioDistList, weights)

Arguments

referenceFeatures	The set of features that weighted distance is computed between.
bioDistList	A list of bioDistclass objects. All the objects must contain the set of features selected.
weights	A matrix where the number of columns equals the number of elements included in the bioDistList list.

Value

Returns a list of bioDistWclass objects. Each element in the list returns the weighted distance associated to each row in the "weights" matrix.

Author(s)

David Gomez-Cabrero

Examples

data(STATegRa_S1)
data(STATegRa_S2)
require(Biobase)

# Truncate data for brevity
Block1 <- Block1[1:100,]
Block2 <- Block2[1:100,]

## Create ExpressionSets
mRNA.ds <- createOmicsExpressionSet(Data=Block1,pData=ed,pDataDescr=c("classname"))
miRNA.ds <- createOmicsExpressionSet(Data=Block2,pData=ed,pDataDescr=c("classname"))

## Create the bioMap  
map.gene.miRNA<-bioMap(name = "Symbol-miRNA",
                       metadata =  list(type_v1="Gene",type_v2="miRNA",
                                        source_database="targetscan.Hs.eg.db",
                                        data_extraction="July2014"),
                       map=mapdata)  

# Create Gene-gene distance computed through miRNA data
bioDistmiRNA<-bioDist(referenceFeatures = rownames(Block1),     
                      reference = "Var1",
                      mapping = map.gene.miRNA,
                      surrogateData = miRNA.ds,  ### miRNA data
                      referenceData = mRNA.ds,  ### mRNA data
                      maxitems=2,
                      selectionRule="sd",
                      expfac=NULL,
                      aggregation = "sum",
                      distance = "spearman",
                      noMappingDist = 0,
                      filtering = NULL,
                      name = "mRNAbymiRNA")

# Create Gene-gene distance through mRNA data
bioDistmRNA<-new("bioDistclass",
                 name = "mRNAbymRNA",
                 distance = cor(t(exprs(mRNA.ds)),method="spearman"),
                 map.name = "id",
                 map.metadata = list(),
                 params = list())

###### Generation of the list of Surrogated distances.

bioDistList<-list(bioDistmRNA,bioDistmiRNA)
sample.weights<-matrix(0,4,2)
sample.weights[,1]<-c(0,0.33,0.67,1)
sample.weights[,2]<-c(1,0.67,0.33,0)

###### Generation of the list of bioDistWclass objects.

bioDistWList<-bioDistW(referenceFeatures = rownames(Block1),
                       bioDistList = bioDistList,
                       weights=sample.weights)

###### Plot of distances.
bioDistWPlot(referenceFeatures = rownames(Block1) ,
             listDistW = bioDistWList,
             method.cor="spearman")
             
###### Computing the matrix of features/distances associated.

fm<-bioDistFeature(Feature = rownames(Block1)[1] ,
                   listDistW = bioDistWList,
                   threshold.cor=0.7)
bioDistFeaturePlot(data=fm)

llrs/STATegRa documentation built on May 29, 2019, 3:42 a.m.