Path_Detail-class: Path_Detail class

In biodev/packageDir: Tool for in silico functional analysis design and exploration of relation between genomic function and aberration.

Description

Contains all information relevent to cellular pathways used in pathway analysis.

Fields

name:

Object of class "character" The name of the pathway repository used.

file:

Object of class "character" The file from which the pathway repostory was loaded.

date:

Object of class "character" The date the pathway repository was loaded.

info:

Object of class "character" Any additional information reguarding the pathway repository.

source:

Object of class "character" The source of the pathway repository. For example, Reactome, via the graphite bioconductor package )

graphite:

Depricated. Only here for legacy purposes.

gene_overlap_counts:

Object of class "matrix" One column, with row names given as gene names. Values are the number of pathways each gene belongs to.

full_path_length:

Object of class "matrix" One column, pathway names given as row names. Values given as the number of genes annotated to each pathway.

symtable:

Object of class "data.frame" The official, approved set of symbols or gene identifiers and any cross references.

paths:

Object of class "matrix" The actual storage of pathways in bipartate graph format, with row names as the path names, column names as gene identifiers and values logical representing gene membership in pathawys.

symbol_type:

Object of class "character" The type of gene identiers used, for example HUGO or Uniprot.

biodev/packageDir documentation built on Nov. 4, 2019, 7:19 a.m.