Do.full.annotation.matrix: Do full annotation matrix

In gecko515/HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs

Description

High-level function to obtain a full annotation matrix, that is a matrix in which the transitive closure of annotations was performed, respect to a given weighted adjacency matrix.

Usage

Do.full.annotation.matrix(anc.file.name = anc.file.name,
  anc.dir = anc.dir, net.file = net.file, net.dir = net.dir,
  ann.file.name = ann.file.name, ann.dir = ann.dir,
  output.name = output.name, output.dir = output.dir)

Arguments

anc.file.name	name of the file containing the list for each node the list of all its ancestor (without rda extension).
anc.dir	relative path to directory where the ancestor file is stored.
net.file	name of the file containing the weighted adjacency matrix of the graph (without rda extension).
net.dir	relative path to directory where the weighted adjacency matrix is stored.
ann.file.name	name of the file containing the matrix of the most specific annotations (without rda extension).
ann.dir	relative path to directory where the matrix of the most specific annotation is stored.
output.name	name of the output file without rda extension.
output.dir	relative path to directory where the output file must be stored.

Value

a full annotation matrix T, that is a matrix in which the transitive closure of annotations was performed. Rows correspond to genes of the input weighted adjacency matrix and columns to terms. T[i,j]=1 means that gene i is annotated for the term j, T[i,j]=0 means that gene i is not annotated for the term j.

See Also

full.annotation.matrix

Examples

data(graph);
data(labels);
data(wadj);
anc <- build.ancestors(g);
tmpdir <- paste0(tempdir(),"/");
save(g, file=paste0(tmpdir,"graph.rda"));
save(L, file=paste0(tmpdir,"labels.rda"));
save(W, file=paste0(tmpdir,"wadj.rda"));
save(anc, file=paste0(tmpdir,"ancestors.rda"));
anc.dir <- net.dir <- ann.dir <- output.dir <- tmpdir;
anc.file.name <- "ancestors";
net.file <- "wadj";
ann.file.name <- "labels";
output.name <- "full.ann.matrix";
Do.full.annotation.matrix(anc.file.name=anc.file.name, anc.dir=anc.dir, net.file=net.file, 
   net.dir=net.dir, ann.file.name=ann.file.name, ann.dir=ann.dir, output.name=output.name, 
    output.dir=output.dir);

gecko515/HEMDAG documentation built on Oct. 18, 2019, 6:34 a.m.