specific.annotation.matrix {HEMDAG} | R Documentation |
Specific annotation matrix
Description
Build the annotation matrix of the most specific functional terms.
Usage
specific.annotation.matrix(file = "gene2pheno.txt.gz")
Arguments
file |
text file representing the associations gene-OBO terms. The file must be written as sequence of rows. Each row represents a gene/protein and all its associations with an ontology term (pipe separated), i.e. in the form e.g.: gene1 |obo1|obo2|...|oboN. |
Details
The input plain text file (representing the associations gene-OBO terms) can be obtained by cloning the GitHub repository obogaf-parser, a perl5 module specifically designed to handle HPO and GO obo file and their gene annotation file (gaf file).
Value
The annotation matrix of the most specific annotations (0/1): rows are genes and columns are functional terms (such as GO or HPO).
Let's denote the labels matrix. If
, means that the gene
is annotated with the class
, otherwise
.
Examples
gene2pheno <- system.file("extdata/gene2pheno.txt.gz", package="HEMDAG");
spec.ann <- specific.annotation.matrix(file=gene2pheno);