biomaRt does not convert entrez gene id to ensembl gene id

biomaRt does not convert entrez gene id to ensembl gene id

0

I am trying to convert my entrez gene_id to ensembl gene_id. Here is my R codes


> library(biomaRt)

> ensembl<- useEnsemblGenomes(biomart = "plants_mart")

> searchDatasets(ensembl,pattern = "Beta")

             dataset                         description
14 bvulgaris_eg_gene Beta vulgaris genes (RefBeet-1.2.2) version 14 RefBeet-1.2.2

> ensembl<- useEnsemblGenomes(biomart = "plants_mart", dataset = "bvulgaris_eg_gene")

> filters= listFilters(ensembl)

> attributes= listAttributes(ensembl)

> View(filters)

> View(attributes)

> genes<- c("LOC104882799","gene-LOC104893862","LOC104890217","LOC104890218","LOC104890219","gene-LOC104890216","gene-LOC104890218","gene-LOC104890219","LOC104890216","104890218","104890219","104890217","104890216") # my NCBI gene_ids normally starts with "gene-" but i editted them differently in order to find the right representation of entrez gene_id

> getBM(attributes = c('entrezgene_id','ensembl_gene_id'), filters="entrezgene_id", values = genes, mart = ensembl)

[1] entrezgene_id   ensembl_gene_id 
<0 rows> (or 0-length row.names)

> getBM(attributes = c('entrezgene_accession','ensembl_gene_id'), filters="entrezgene_accession", values = genes, mart = ensembl)

[1] entrezgene_accession ensembl_gene_id     
<0 rows> (or 0-length row.names)

What am i doing wrong?


biomaRt


ensembl


entrez


NCBI

• 409 views

updated 1 hour ago by

&starf;

1.7k

written 3 months ago by

0

Read more here: Source link

Tagged