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library("ctc");
library("ape");
get_cluster_info = function( Rdata_file ) {
load(Rdata_file);
ordered_genes_file = paste(Rdata_file, ".ordered_gene_matrix", sep='');
ordered_genes = hc_genes$data;
write.table(ordered_genes, file=ordered_genes_file, quote=F, sep="\t");
gene_tree = hc2Newick(hc_genes);
gene_tree_filename = paste(Rdata_file, ".gene_tree", sep='');
write(gene_tree, file=gene_tree_filename);
# get rid of the distances since these can sometimes cause problems with other software tools.
gene_nodist_tree_filename = paste(Rdata_file, ".gene_nodist_tree", sep='');
t = read.tree(text=gene_tree);
t$edge.length = NULL;
write.tree(t, file=gene_nodist_tree_filename);
sample_tree = hc2Newick(hc_samples);
sample_tree_filename = paste(Rdata_file, ".sample_tree", sep='');
write(sample_tree, file=sample_tree_filename);
}
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