bioMart biotype assignment

0

Hello,

I am trying to assign bio-types to genes that I obtained after differential expression analysis. I used biomart for this purpose, but it retrieves only 54000 genes, whereas my expression data contains 57000 genes.

library(biomaRt)
ensembl = useEnsembl("ensembl",dataset="hsapiens_gene_ensembl", mirror = "useast")
genes <- df_RNA$gene_id
G_list <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id",
                                                          "entrezgene_id", "hgnc_symbol", "gene_biotype"), values=substr(genes, 1, 15), mart=ensembl)

What can be the possible error here, also what alternative to biomart can be used?


biomart

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