R/Variance_selection.R

In RaikOtto/artdeco: Alikeness Based on Regression on Transciptome DECOnvolution

variance_filtering = function(expr_raw){
    
    hgnc_list = row.names(expr_raw)
    expr_raw = expr_raw[ ! is.na(hgnc_list),]
    expr_raw = expr_raw[ hgnc_list != "",]
    hgnc_list = hgnc_list[!is.na(hgnc_list)]
    hgnc_list = hgnc_list[hgnc_list != ""]
    
    hgnc_list = str_to_upper(hgnc_list)
    hgnc_list_uni = as.character( unique(hgnc_list) )
    
    max_list <<- as.integer( sapply( hgnc_list_uni, FUN = function(gene){
      var_match = which( hgnc_list == gene )
      if (length(var_match) > 1){
            row_var_max = which.max( 
                apply( 
                    matrix(
                        as.integer(
                            as.character(
                                unlist(
                                    expr_raw[var_match,]
                                )
                            )
                        ),
                        ncol = length(var_match)
                    ),
                    FUN = var,
                    MARGIN = 2
                )
            );
            } else{ 
              row_var_max = 1
              }
      return( var_match[row_var_max] )
    }))
    
    max_list[is.na(max_list)] = 0
    expr_raw = expr_raw[max_list,]
    rownames(expr_raw) = hgnc_list[as.integer(max_list)]
    colnames(expr_raw) = str_replace(colnames(expr_raw), pattern = "^X", "")
    
    return( expr_raw )
}