map_gene_annot: Convert gene identifiers with AnnotationHub

In vitkl/ParetoTI: R toolbox for Archetypal Analysis and Pareto Task Inference on single cell data

Description

map_gene_annot() Maps gene annotations using OrgDb databases from AnnotationHub. Most useful for mapping gene identifiers. This function can pick one mapped annotation for each key.

Usage

map_gene_annot(taxonomy_id = 9606, keys = "TP53",
  columns = c("ENSEMBL"), keytype = "SYMBOL", pick_one = TRUE,
  localHub = FALSE, return_org_db = FALSE,
  ann_hub_cache = AnnotationHub::getAnnotationHubOption("CACHE"))

Arguments

taxonomy_id	Taxonomy id of your species. 9606 is human, 10090 is mouse. Find your species id using taxonomy search by UniProt: https://www.uniprot.org/taxonomy/.
keys	gene or protein identifiers of keytype
columns	columns to retrieve. Details: colsAndKeytypes.
keytype	type of keys identifiers. Use keytypes(map_gene_annot(taxonomy_id = 9606, return_org_db = T)) to find which keytypes are available. Most frequent options: "ENSEMBL", "SYMBOL", "ALIAS".
pick_one	pick one mapped annotation (from columns) for each key. Works only with one column.
localHub	set localHub = FALSE for working offline. Details AnnotationHub.
return_org_db	return OrgDb database link instead of gene annotations.
ann_hub_cache	If needed, set location of local AnnotationHub cache to specific directory by providing it here. To view where cache is currently located use getAnnotationHubOption("CACHE")

Value

data.frame containing mapped identifiers

vitkl/ParetoTI documentation built on Feb. 11, 2020, 1:36 a.m.