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

Description Usage Arguments Value See Also Examples

Filtering genes which are widely expressed in most of the cell population.

1	GeneFilter(obj)

obj

The list object from function ModalFilter

\res

dataThe raw expresion data after filter widly expressed genes \resgeneSummA data frame including gene names as, corresponding number of expressed cells and the peak number of probability density distribution function \rescellSummA data frame including cell ID and corresponding number of expressed genes \resbinadataThe binary expression matrix corresponding to raw data

ModalFilter

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)


## The function is currently defined as
function (obj) 
{
    maxexp = dim(obj$newdata)[2]
    data(excludeGene)
    excludeGene = as.character(excludeGene[, 1])
    geneSumm = obj$geneSumm
    index = match(geneSumm$gene, excludeGene)
    geneSumm = geneSumm[is.na(index), ]
    data = obj$newdata
    index = match(geneSumm$gene, row.names(data))
    data = data[index, ]
    binadata = obj$binadata
    binadata = binadata[index, ]
    geneindex = rowSums(binadata)
    binadata = binadata[geneindex < maxexp, ]
    data = data[geneindex < maxexp, ]
    geneSumm = geneSumm[geneindex < maxexp, ]
    obj$newdata = data
    obj$geneSumm = geneSumm
    obj$binadata = as.matrix(binadata)
    return(obj)
  }