samples function and generics

[nsheff]

the bioconductor Biobase package creates a generic samples function:

https://github.com/Bioconductor/Biobase/blob/2845fa44788b8379f931fa0a19c6812fb1dd453b/R/AllGenerics.R#L60

This makes it so if you load Biobase after BiocProject, it fails:

library(BiocProject)
library(Biobase)
bp = BiocProject::BiocProject("/home/ns5bc/code/dura_macs/metadata/config.yaml", subproject="atac")
samples(bp)

Returns:

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘samples’ for signature ‘"SimpleList"’

and:

Attaching package: ‘Biobase’

The following object is masked from ‘package:BiocProject’:

    samples

The following object is masked from ‘package:pepr’:

    samples

it works if you load BiocProject after Biobase, but then samples can't work on a MIAME object:

> samples(m)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘samples’ for signature ‘"MIAME"’
> Biobase::samples(m)
list()
> class(m)
[1] "MIAME"
attr(,"package")
[1] "Biobase"

Is there any way to make these place nicely?

[nsheff]

information here: http://adv-r.had.co.nz/S4.html
maybe we need to link into the existing generic and have biocproject import biobase

[stolarczyk]

using

setGeneric("samples", getGeneric("samples", package="Biobase"))

in BiocProject package is not possible, as the devtools::check and even just attaching BiocProject package throws warnings that say:

Warning: multiple methods tables found for ‘samples’
     Warning: replacing previous import ‘Biobase::samples’ by ‘pepr::samples’ when loading ‘BiocProject’

and

Warning: replacing previous import ‘Biobase::samples’ by ‘pepr::samples’ when loading ‘BiocProject’

but redefining the generic in pepr both solves the issue in BiocProject and does not trigger any warnings when attaching/checking pepr

Yet, all the functionality is there:

> samples(bp)
      sample_name               file_path
1:    laminB1Lads    data/laminB1Lads.bed
2: vistaEnhancers data/vistaEnhancers.bed
> m=Biobase::MIAME()
> samples(m)
list()

Do we go this route?

[stolarczyk]

Even if the former worked we'd run into the same issue when using pepr::samples with Biobase loaded

BiocProject just maps this method to the Annotated class

[nsheff]

this causes pepr to depend on biobase though, correct? we don't want to do that...

isn't there a way to keep pepr independent, but allow biocproject to attach the pepr function to the biobase generic for annotated objects?

[stolarczyk]

this causes pepr to depend on biobase though, correct?

yes