Hervé Pagès

Actually, it's also broken when the right value is a matrix: ``` > ab ab[2:4, ] ab DataFrame with 4 rows and 2 columns a b 1 11 21 2...

It seems to me that coercion from character matrix to DataFrame should be fixed in general, not just in the context of coercing the RHS to DataFrame. Other coercions from...

Thanks Michael. Will take a look after the release.

You don't see them but the metadata columns are here: ``` library(GenomicRanges) gr1

> But then why is the output of subtract of two Geanges a GRangesList instead of GRanges? Because each range in the 1st GRanges object can produce several fragments after...

In that case you need to manually propagate the top-level metadata columns of the GRangesList object to its unlisted form. This can be done with: ``` x

@jwokaty What should we do with this PR?

Please remove [this line](https://github.com/hsadia538/GenomicRanges/blob/1ecc930b38d78cb5dd40739f4071a6625fe60620/vignettes/ExtendingGenomicRanges.Rmd#L74-L75). The **MutableRanges** package is an abandonned project that never made it to Bioconductor. Thanks!

@hsadia538 Are you going to be able to make that change?

@yeyuan98 > I guess the end user should prune the subject on their own before feeding the subject into this function. Not totally satisfactory. We need to take a close...