#' @name sd.filter
#' @aliases sd.filter,Rscexv-method
#' @rdname sd.filter-methods
#' @docType methods
#' @description This function is removing cells and genes that do not show any variation in the data.
#' @param dataObj the Rscexv object
#' @title description of function sd.filter
#' @export
setGeneric('sd.filter', ## Name
function (dataObj) {
standardGeneric('sd.filter')
}
)
setMethod('sd.filter', signature = c ('Rscexv'),
definition = function (dataObj) {
sds1 <- NULL
sds2 <- NULL
sds1 <- apply(dataObj@data,1,sd)
sds2 <- apply(dataObj@data,2,sd)
cuto1 <- which(sds1==0)
cuto2 <- which(sds2==0)
if(length(cuto1) >0){
write ( colnames(dataObj@data)[cuto2], file="./filtered_samples.txt",ncolumn=1, append=T )
dataObj <- remove.samples(dataObj, cuto1 )
}
if(length(cuto2) >0){
write ( colnames(dataObj@data)[cuto2], file="./filtered_genes.txt",ncolumn=1, append=T )
dataObj <- remove.genes(dataObj, cuto2 )
}
dataObj
}
)
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