getGeneLengthAndGCContent in EDASeq complains about Ensemble gene ID

I am trying to use the getGeneLengthAndGCContent function from the EDASeq library to retrieve gene lengths for c. elegans. I retrieved Ensemble gene ids from Biomart for c.elegans and I'm using those as input to getGeneLengthAndGCContent (I picked "ensemble_gene_id" from the filters of the worm annotation Mart). Here's an example of how I'm trying to use the function:

getGeneLengthAndGCContent("WBGene00001042", org, mode=c("biomart", "org.db"))

When I try to run this, I get

Error in getGeneLengthAndGCContent("WBGene00001042", org, mode = c("biomart",  : 
  Only ENTREZ or ENSEMBL gene IDs are supported.

However, it does seem to me like WBGene00001042 is an Ensembl ID (here's an example of a c elegans gene in Ensembl: http://uswest.ensembl.org/Caenorhabditis_elegans/Gene/Summary?g=WBGene00001042;r=III:5415556-5419565;t=W03A5.7.1) I don't see any other possible ids in Ensembl (I tried gene name, that didn't work either)

EDIT: Scrolling down to the bottom of the page, there is a table which includes "coding sequence length." I am now trying to figure out how to retrieve this independent of getGeneLengthAndGCContent

gene r

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updated 3.1 years ago by Ram

• written 6.1 years ago by An Ignorant Wanderer •

1 answer

The source code which you can download from Bioconductor indicates that this error is thrown when the function cannot auto-detect the ID type, so ENTREZ or Ensembl. It is the script getLengthAndGC.R and in this lines 19-21.

The auto-check function for the gene names is:

function(id)
{
    type <- NA
    if(grepl("^[Ee][Nn][Ss][A-Za-z]{0,3}[Gg][0-9]+", id)) type <- "ensembl"
    else if(grepl("^[0-9]+$", id)) type <- "entrez"
    else if(grepl("^[Yy][A-Za-z]{2}[0-9]{3}[A-Za-z]", id)) type <- "sgd"
    else if(grepl("^[Aa][Tt][0-9][A-Za-z][0-9]{5}", id)) type <- "tair"
    return(type)
}

Obviously your gene name escaped this classification.

Simple workaround is to turn off this check by replacing lines 19-21 with:

#id.type <- .autoDetectGeneIdType(id[1])
id.type<-"ensembl"
#ifis.na(id.type))
#    stop("Only ENTREZ or ENSEMBL gene IDs are supported.")

You don't even need the entire package, this function alone is sufficient to retrieve the information you want:

> getGeneLengthAndGCContent("WBGene00001042", "cel")
Connecting to BioMart ...
Downloading sequence ...
      length           gc 
1329.0000000    0.3069977

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written 6.1 years ago by ATpoint