comparison cluster.tools/extract.cons.cluster.from.result.R @ 7:2efa1a284546 draft

Uploaded

6:3d3a8595b981

load( opt$results.file )
cons.matrices <- lapply( results[ 2:length(results) ], '[[', 'consensusMatrix' )
cls <- lapply( results[ 2:length(results) ], '[[', 'consensusClass' )
names( cons.matrices ) <- names( cls ) <- 2:length( results )

ch.k.select <- as.character( opt$k.select )
if ( ch.k.select %in% names( cls ) ) {
  ## get the consensusClass file that's associated with the k.select
  cl <- cls[[ ch.k.select  ]] 

    write.table( cl, opt$cluster.class.out, sep="\t", row.names=FALSE, quote=FALSE )
  } else if ( ! is.null( opt$output.select.rdata ) ) {
    ## re-order the samples to follow the cluster assignment
    treecl.res <- results[[ opt$k.select ]]$consensusTree
    select.result <- results[[ opt$k.select ]]
    save( file=opt$output.select.rdata, treecl.res, cl, select.result, data )
  } else {
    stop( 'no valid output format specified\n' )
  }
} else {

7:2efa1a284546

load( opt$results.file )
cons.matrices <- lapply( results[ 2:length(results) ], '[[', 'consensusMatrix' )
cls <- lapply( results[ 2:length(results) ], '[[', 'consensusClass' )
names( cons.matrices ) <- names( cls ) <- 2:length( results )
save.image( '~/tmp/extract.dbg.rda' )
ch.k.select <- as.character( opt$k.select )
if ( ch.k.select %in% names( cls ) ) {
  ## get the consensusClass file that's associated with the k.select
  cl <- cls[[ ch.k.select  ]] 

    write.table( cl, opt$cluster.class.out, sep="\t", row.names=FALSE, quote=FALSE )
  } else if ( ! is.null( opt$output.select.rdata ) ) {
    ## re-order the samples to follow the cluster assignment
    treecl.res <- results[[ opt$k.select ]]$consensusTree
    select.result <- results[[ opt$k.select ]]
    
    if ( length(cl) == ncol(data) ) {
      names( cl ) <- treecl.res$labels <- select.result$consensusTree$labels <- colnames(data)
    } else if ( length(cl) == nrow(data) ) {
      names( cl ) <- treecl.res$labels <- select.result$consensusTree$labels <- rownames(data)
    } else {
      stop( "Number of clustered elements not equal to either number of rows or columns of data matrix\n" )
    }
    
    save( file=opt$output.select.rdata, treecl.res, cl, select.result, data )
  } else {
    stop( 'no valid output format specified\n' )
  }
} else {