Fethcing HGNC symbols using R package biomaRt

I am trying to collect the HGNC symbols for genes after some high throughput RNAseq, but the syntax isn't functioning, can anyone pick out the error or tell me how to do this please?

Running biomaRt, on R/4.0.0

my syntax

  dds_covid_df<- sapply( strsplit( rownames(dds_covid), split="\\+" ), "[", 1 )
  ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", )
  genemap <- getBM( attributes = c("ensembl_gene_id_version", "hgnc_symbol"), filters = "ensembl_gene_id_version", values = dds_covid_df, mart = ensembl)
                    filters = "ensembl_gene_id",
                    values = m,
                    mart = ensembl )
  idx <- match( dds_covid_df, genemap$ensembl_gene_id )
dds_covid$hgnc_symbol <- genemap$hgnc_symbol[ idx ]

I am trying to collect the HGNC symbols for genes after some high throughput RNAseq, but the syntax isn't functioning, can anyone pick out the error or tell me how to do this please?

dds_covid is my dataframe

Running biomaRt, on R/4.0.0

my syntax

dds_covid_df<- sapply( strsplit( rownames(dds_covid), split="\\+" ), "[", 1 )
  ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", )
  genemap <- getBM( attributes = c("ensembl_gene_id_version", "hgnc_symbol"), filters = "ensembl_gene_id_version", values = dds_covid_df, mart = ensembl)
                    filters = "ensembl_gene_id",
                    values = m,
                    mart = ensembl )
  idx <- match( dds_covid_df, genemap$ensembl_gene_id )
dds_covid$hgnc_symbol <- genemap$hgnc_symbol[ idx ]

my results

 Gene_ID hgnc_symbol
1    ENSG00000242268.3          NA
2    ENSG00000270112.4          NA
3    ENSG00000280143.1          NA
4   ENSG00000146083.12          NA
5    ENSG00000263642.1          NA
6    ENSG00000225275.4          NA
7   ENSG00000158486.13          NA
8    ENSG00000283967.1          NA
9    ENSG00000273639.6          NA

r biomart rna-seq

• 1,367 views • link

updated 5.7 years ago by Kevin Blighe

• written 5.7 years ago by omicsnstuff •

1 answer

Hi,

You just need to 'knock off' (remove) that number at the end of each Ensembl gene ID, which relates to the ID version (I think). Something like:

sub('\\.[0-9]*$', '', m)

Kevin

• 0 views • link

written 5.7 years ago by Kevin Blighe

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