geneInfo: Simple Feature Annotation

In renozao/xbioc: Extra Base Functions for Bioconductor

Description

Simple Feature Annotation

Usage

geneInfo(
  x,
  annotation = "human",
  extras = c("biogps", "ncbi", "pathway", "kegg")
)

Arguments

x	feature identifiers to annotate
annotation	Annotation package to use. It can be the name of an annotation package or of an organism supported by biocann_orgdb. It can also be a AnnDbBimap object that converts the features into ENTREZID, e.g., org.Hs.egSYMBOL2EG.
extras	Indicates the type of information/resource to add for each feature. Out-links to online resource can be added the prefix '~' to selected resources. Note that the resources 'NCBI' and 'bioGPS' are de facto online resources, and make ENTREZID and SYMBOL as links to the respective gene page.

See Also

biocann_orgdb

Examples

# Entrez IDs
geneInfo(1:5)
geneInfo(1:5, extras = 'bioGPS')

# probe ids
ids <- c("1007_s_at", "1053_at", "117_at", "121_at", "not_a_probe_id")
geneInfo(ids, 'hgu133plus2.db')
geneInfo(ids, 'hgu133plus2.db', extras = 'bioGPS')
geneInfo(ids, 'hgu133plus2.db', extras = 'pathway')

renozao/xbioc documentation built on Sept. 3, 2020, 1:13 a.m.