getMEN: Mutually nearest exclusive gene pairs

In Fang0828/SCMarker: What the package does (short line)

Usage

getMEN(HamDD, genename, k, n)

Arguments

HamDD	A matrix from multiplicate of binary data tcrossprod((1 - binadata), binadata).
genename	The rownames and colnames of matrix HamDD
k	The maximum number that how many nearest neighbors would be considered.
n	The minimum number which is the coexpressed cells for each gene pairs

Value

A list including the MNN nearest neighbors which mutually exclusive in more than MNNindex samples.

Examples

data(melanoma)
melanoma1=as.matrix(melanoma[,2:dim(melanoma)[2]])
row.names(melanoma1)=melanoma[,1]
res=ModalFilter(data=melanoma1,geneK=10,cellK=10,width=2,cutoff=2)
res=GeneFilter(obj=res)
data = res$newdata
binadata = res$binadata
genename = row.names(binadata)
HamDD = tcrossprod((1 - binadata), binadata)
marker = getMEN(HamDD = HamDD, genename = genename,
        k = 200, n = 20)

## The function is currently defined as
function (HamDD, genename, k, n)
{
    MNNgene = lapply(1:dim(HamDD)[1], RankGene, k = k, HamD = HamDD,
        geneName = genename, n = n)
    genePair = unique(as.character(do.call(cbind, lapply(1:length(MNNgene),
        MNNpair, MNNgene = MNNgene, geneName = genename))))
    return(genePair)
  }

Fang0828/SCMarker documentation built on May 13, 2019, 12:51 p.m.