convertGeneIdentifiers {psichomics} | R Documentation |
Convert gene identifiers
convertGeneIdentifiers( annotation, genes, key = "ENSEMBL", target = "SYMBOL", ignoreDuplicatedTargets = TRUE )
annotation |
|
genes |
Character: genes to be converted |
key |
Character: type of identifier used, e.g. |
target |
Character: type of identifier to convert to; read
|
ignoreDuplicatedTargets |
Boolean: if |
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.
Other functions for gene expression pre-processing:
filterGeneExpr()
,
normaliseGeneExpression()
,
plotGeneExprPerSample()
,
plotLibrarySize()
,
plotRowStats()
# Use species name to automatically look for a OrgDb database sp <- "Homo sapiens" genes <- c("ENSG00000012048", "ENSG00000083093", "ENSG00000141510", "ENSG00000051180") convertGeneIdentifiers(sp, genes) convertGeneIdentifiers(sp, genes, key="ENSEMBL", target="UNIPROT") # 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(sp, genes) convertGeneIdentifiers(sp, genes, key="ENSEMBL", target="UNIPROT")