Hi there,

I am using GenomicInteractions package to read in the bedpe file.

There are several columns for meta data and I did not find a way to add them.

if I use:

mydata<- makeGenomicInteractionsFromFile("my.bedpe" , 
                                type="bedpe", 
                                experiment_name="my test", 
                                description="test")

meta<- read.table("my.bedpe")

meta<- meta[, 11:13]

mcols(mydata)<- meta

it throws me an error:

Error in `elementMetadata<-`(x, ..., value = value) : 
  replacement 'elementMetadata' value must be a DataTable object or NULL

But I can add the meta to a GRange object without problem:

gr<- anchorOne(mydata)

mcols(gr)<- meta

Thanks and happy new year!

Ming

At first I was surprised by this question, since we do not use data.table to import bedpe files in our package. It turns out the answer is hiding in the way S4Vectors handles metadata.

The quick solution is to give mcols what it wants, which in this case in a DataFrame:

mcols(mydata) <- DataFrame(meta)

GenomicInteractions is based around the "Vector"<font face="monospace"> c</font>lass from the S4Vectors core package, which is where all of the mcols functionality is handled. Bioconductor-developed classes store metadata in a DataFrame object, which is a bioconductor-specific class based around DataTable. The GRanges mcols methods appears to perform this conversion implicitly. I am not sure why the mcols(granges) method is different from the mcols(GenomicInteractions) method, I will email the development list about it.

This will probably be fixed in the next version of GenomicInteractions, because we will use InteractionSet underneath our class which will change a lot of implementation details, although this also uses Vector so the fix might have to be upstream.

Hope that helps,

Malcolm