intersectoR-methods: Generic intersectoR function

In genesofeve/ProjectR: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering

Generic intersectoR function

Description

A function to find and test the intersecting values of two sets of objects, presumably the genes associated with patterns in two different datasets. Both the input objects need to be of the same type either kmeans or hclust.

Usage

intersectoR(pSet1, pSet2, pval, ...)

## S4 method for signature 'kmeans,kmeans'
intersectoR(pSet1 = NA, pSet2 = NA, pval = 0.05, full = FALSE)

## S4 method for signature 'hclust,hclust'
intersectoR(pSet1 = NA, pSet2 = NA, pval = 0.05, full = FALSE, k = NULL)

Arguments

pSet1	an object for a set of patterns where each entry is a set of genes associated with a single pattern
pSet2	an object for a second set of patterns where each entry is a set of genes associated with a single pattern
pval	the maximum p-value considered significant
...	additional parameters depending on input object
full	logical indicating whether to return full data frame of signigicantly overlapping sets. Default is false will return summary matrix.
k	Numeric giving cut height for hclust objects, if a vector is given arguments will be applied to pSet1 and pSet2 in that order

Value

A list containing: Overlap matrix, overlap index, and overlapping sets.

Examples

ESepiGen4c1lmRNASeq <- p.ESepiGen4c1l$mRNA.Seq
rownames(ESepiGen4c1lmRNASeq) <- map.ESepiGen4c1l$GeneSymbols

k.RNAseq6l3c3t<-kmeans(p.RNAseq6l3c3t,22)
k.ESepiGen4c1l<-kmeans(ESepiGen4c1lmRNASeq,10)
intersectoR(k.RNAseq6l3c3t, k.ESepiGen4c1l, pval=.05)

h.RNAseq6l3c3t<-hclust(as.dist(1-(cor(t(p.RNAseq6l3c3t)))))
h.ESepiGen4c1l<-hclust(as.dist(1-(cor(t(ESepiGen4c1lmRNASeq)))))
intersectoR(pSet1=h.ESepiGen4c1l, pSet2=h.RNAseq6l3c3t, pval=.05, k=c(3,4))

genesofeve/ProjectR documentation built on Nov. 16, 2024, 8:20 p.m.