Add Filter Gene Expression Function

[tinyheero]

A function to filter out lowly expressed genes based on some user-defined threshold would be useful. For instance,

filterGeneExprsMat <- function( mat, prop = 0.2, thres = log2(10), returnFlags = FALSE ){
  # require('genefilter')
  if ( ncol(as.matrix(mat)) > 1 ){
    filterFlag <- apply( mat, 1, function(x){
      ifelse( sum(x >= thres)/length(x) >= prop, TRUE, FALSE )
    })
  } else{
    filterFlag <- (mat >= thres)
  }
  if ( returnFlags ){
    return( filterFlag )
  } else{
    return( mat[ filterFlag, ] )
  }
}