'Missing genes in converting "ensembl_gene_id_version" to "ensembl_gene_id" in biomaRt package
I am using biomaRt package to convert "ensembl_gene_id_version" to "ensembl_gene_id" but unfortunately I have some missing genes. The empty values for the rest are because there's no mapping between Ensembl ID and HGNC name for those genes.
How can I solve this problem?
Thanks in advance
mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
gene_ids_version <- rownames(diff)
diffensembl <- getBM(attributes = c('ensembl_gene_id_version', 'hgnc_symbol'), filters =
'ensembl_gene_id_version', values = gene_ids_version, mart = mart)
library(stringr)
gene_ids <- str_replace(gene_ids_version, pattern = ".[0-9]+$", replacement = "")
diffensembl <- getBM(attributes = c('ensembl_gene_id', 'hgnc_symbol'), filters =
'ensembl_gene_id', values = gene_ids, mart = mart)
Sources
This article follows the attribution requirements of Stack Overflow and is licensed under CC BY-SA 3.0.
Source: Stack Overflow
| Solution | Source |
|---|
