biomaRt::getSequence - Invalid type argument

Question

[mbk0asis]

Hi, all!

I'm trying to download peptide sequence using biomaRt::getSequence() function.

The code I used is like below,

seq = getSequence(id = c("ENSP00000367848"), 
                  type = "ensembl", 
                  seqType = "peptide", 
                  mart = mart)

When I ran it, I got a following error.

Error in getSequence(id = c("ENSP00000367848"), type = "ensembl", seqType = "peptide",  : 
      Invalid type argument.  Use the listFilters function to select a valid type argument.

According to its vignette, "Supported types are hugo, ensembl, embl, entrezgene, refseq, ensemblTrans and unigene."

Why am I getting this error? Can you guys help me?

Thank you!

Answer 1

[Ram]

The type you need is emsembl_peptide_id. The list of supported types are not valid as exact string values, I think.

[mbk0asis]

Thank you, RamRS!

You are right the list in the vignette doesn't match to actual values.

Where did you find the actual type values?

[Ram]

Like the error message says, you can run listFilters(mart) to get a list of filters (which are also valid values for the type parameter) with their descriptions.