library("AnnotationDbi")
library("org.Hs.eg.db")
anno_df$gene_name <- mapIds(org.Hs.eg.db,
- keys=anno_df$gene_id,
- column="SYMBOL",
- keytype="ENSEMBL",
- multiVals="first")
Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.
•
written
by
abradford •
One can interpret the error literally, i.e., none of the values of anno_df$gene_id relate to Ensembl gene IDs. Can you show the output of str(anno_df$gene_id), please?
It looks like you are using the airway dataset. One can convert the Ensembl gene IDs in this dataset to gene symbols via:
library(airway)
data('airway')
# Annotate the Ensembl gene IDs to gene symbols:
ens <- rownames(airway)
library(org.Hs.eg.db)
symbols <- mapIds(org.Hs.eg.db, keys = ens,
column = c('SYMBOL'), keytype = 'ENSEMBL')
symbols <- symbols[!is.na(symbols)]
symbols <- symbols[match(rownames(airway), names(symbols))]
rownames(airway) <- symbols
keep <- !is.na(rownames(airway))
airway <- airway[keep,]
...as I do here in my vignette for EnhancedVolcano: https://github.com/kevinblighe/EnhancedVolcano (see Quick Start)
Please also see my answer here: Translating gene names to entrez id's
Kind regards,
Kevin
This is awesome! Thank you. I am trying the conversion code you gave me but here is the output from str(anno_df$gene_id):
chr [1:34528] "5S_rRNA" "7SK" "A1BG" "A1BG-AS1" "A1CF" "A2M" "A2M-AS1" "A2ML1" "A2ML1-AS2" "A2MP1" "A3GALT2" ..
Hi, therein exists the problem, i.e., your keytype should be SYMBOL, not ENSEMBL
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