GeneAnnotations-class: GeneAnnotations class

In priesgo/TCGAome: MultiOmics (just RNAseq and RPPA...) Data Analyzer on TCGA data

Description

An S4 class to represent a set of gene annotations built from tall-skinny table with the columns "Gene" and "Term". This class provides the functionality to compute several useful metrics based on the gene annotations: distance matrix, term frequency of annotation, functional similarity and enrichment.

Slots

raw_annotations

A data.frame having columns "Gene" and "Term" that contains all annotations.

name

The annotations name

gene2term

A data.frame that stores the pivoted annotations across genes

term2gene

A data.frame that stores the pivoted annotations across terms

max_term_annotations

The maximum frequency of annotations, that is the maximum number of terms associated to any gene

func_similarity_methods

Stores the supported similarity methods

priesgo/TCGAome documentation built on May 25, 2019, 11:26 a.m.