Simplify browsing of studies

[lwaldron]

Currently, looking up which studies contributed to a RAV requires something like the following:

> ravc2 <- GenomicSuperSignature::getModel(prior = "C2")
> colData(ravc2)[colData(ravc2)$RAV == "RAV272", "studies"] 
$Cl4764_272
[1] "ERP020977" "SRP039361" "SRP045352"

And then searching for the accession numbers e.g. in the European Nucleotide Browser. And it's more difficult to find the PMIDs of studies contributing to the RAV.

It would be very convenient to have a function that outputs these directly, either with a message saying to search them in the European Nucleotide Browser or giving a direct link (e.g. https://www.ebi.ac.uk/ena/browser/view/ERP020977 for the first ERP above, although ENA browser annoyingly takes you down to the "reads" section of the page). Being able to browse PMIDs of the studies would also be very useful.

[shbrief]

Thanks for the feedback, Levi! For now there are two functions doing what you did above:

> findStudiesInCluster(RAVmodel, 272)
  studyName PC Variance explained (%)
1 ERP020977  1                  30.95
2 SRP039361  2                  13.82
3 SRP045352  1                  21.18
4 SRP045352  2                  17.20

> findStudiesInCluster(RAVmodel, 272, studyTitle = TRUE)
  studyName PC Variance explained (%)
1 ERP020977  1                  30.95
2 SRP039361  2                  13.82
3 SRP045352  1                  21.18
4 SRP045352  2                  17.20
                                                                                                                           title
1                                                         _Genetics_of_gene_expression_in_macrophage_immune_response_Open_access
2 Functional and Transcriptomic Characterization of iPSC-derived Macrophages and their Application in Modeling Mendelian Disease
3                   Comparative Analysis of Transcriptional Responses in Monocytes from Human Neonates, Adults, and Older Adults
4                   Comparative Analysis of Transcriptional Responses in Monocytes from Human Neonates, Adults, and Older Adults

> getRAVInfo(RAVmodel, 272)
$clusterSize
[1] 4

$silhouetteWidth
[1] 0.06

$enrichedPathways
[1] 87

$members
  studyName PC Variance explained (%)
1 ERP020977  1                  30.95
2 SRP039361  2                  13.82
3 SRP045352  1                  21.18
4 SRP045352  2                  17.20

I'll update these to include PMIDs and potentially provide the link to the source data as well.

[lwaldron]

Oh great, sorry I missed those!