R/GetVarGenes.R

In akonturek/MyFirstPackage: Test functions RII course

#'Calculates the top N variable genes from a scell object
#'@param sco An scell S4 object
#'@param nvar The number of genes we wich to retrieve
#'@export get.var.genes
get.var.genes <- function(sco,nvar){

  genes.var <- apply(sco@data,1,var)
  top.var.genes <- names(rev(sort(genes.var))[1:nvar])
  sco@var.genes <- top.var.genes #puts the var genes into a new slot
  sco@tsne <- matrix() #takes into account the number of genes we define, if change the number from 50 to 100 - tsne will be automatically recalculated
  sco #returns the new object
}