org.Hs.egHPPA: Annotations of Human Entrez Genes (EG) by Human Phenotype...

In dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

Description

An R object that contains associations between HPPA terms and Human Entrez Genes. This data is first prepared based on http://purl.obolibrary.org/obo/hp.obo and http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt.

Usage

data(org.Hs.egHPPA)

Value

an object of class "GS", a list with following components:

• set_info: a matrix of nSet X 4 containing gene set information, where nSet is the number of gene sets (i.e. HPPA terms), and the 4 columns are "setID" (i.e. "Term ID"), "name" (i.e. "Term Name"), "namespace" and "distance"

• gs: a list of gene sets, each storing gene members thereof. Always, gene sets are identified by "setID" and gene members identified by "Entrez ID"

References

Robinson et al. (2012) The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet, 83:610-615.

Examples

org.Hs.egHPPA <- dRDataLoader(RData='org.Hs.egHPPA')
names(org.Hs.egHPPA)

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: supraHex
Loading required package: hexbin
'org.Hs.egHPPA' (from package 'dnet' version 1.1.1) has been loaded into the working environment (at 2018-01-23 22:13:33)
[1] "gs"       "set_info"

dnet documentation built on Feb. 20, 2020, 5:08 p.m.