convertGeneIdentifiers: Convert gene identifiers

In nuno-agostinho/cTRAP: Identification of candidate causal perturbations from differential gene expression data

Convert gene identifiers

Description

Convert gene identifiers

Usage

convertGeneIdentifiers(
  genes,
  annotation = "Homo sapiens",
  key = "ENSEMBL",
  target = "SYMBOL",
  ignoreDuplicatedTargets = TRUE
)

Arguments

genes	Character: genes to be converted
annotation	OrgDb with genome wide annotation for an organism or character with species name to query OrgDb, e.g. "Homo sapiens"
key	Character: type of identifier used, e.g. ENSEMBL; read ?AnnotationDbi::columns
target	Character: type of identifier to convert to; read ?AnnotationDbi::columns
ignoreDuplicatedTargets	Boolean: if TRUE, identifiers that share targets with other identifiers will not be converted

Value

Character vector of the respective targets of gene identifiers. The previous identifiers remain other identifiers have the same target (in case ignoreDuplicatedTargets = TRUE) or if no target was found.

Examples

genes <- c("ENSG00000012048", "ENSG00000083093", "ENSG00000141510",
           "ENSG00000051180")
convertGeneIdentifiers(genes)
convertGeneIdentifiers(genes, key="ENSEMBL", target="UNIPROT")

# Explicit species name to automatically look for its OrgDb database
sp <- "Homo sapiens"
genes <- c("ENSG00000012048", "ENSG00000083093", "ENSG00000141510",
           "ENSG00000051180")
convertGeneIdentifiers(genes, sp)

# Alternatively, set the annotation database directly
ah <- AnnotationHub::AnnotationHub()
sp <- AnnotationHub::query(ah, c("OrgDb", "Homo sapiens"))[[1]]
columns(sp) # these attributes can be used to change the attributes

convertGeneIdentifiers(genes, sp)

nuno-agostinho/cTRAP documentation built on March 28, 2024, 3:59 p.m.