search

lianos / multiGSEA

NOTE: This package has been renamed to sparrow and will be submitted to Bioconductor 3.14. Please use that package instead. This is kept here for posterity.
https://lianos.github.io/multiGSEA/
MIT License
21 stars 2 forks source link

Make MSigDB GeneSetDb fetching more robust #2

Open lianos opened 6 years ago

lianos commented 6 years ago

We are hacking together the expected *.rds name for the MSigDB GeneSetDb.* objects based on version, species, and identifiers in the getMSigGeneSetDb function.

The current implementation is flimsy and can be made more robust.

phaverty commented 6 years ago

The README example fails because it looks for GeneSetDb.MSigDB.Hsapiens-entrez.v61.rds, but has GeneSetDb.MSigDB.Hsapiens.v61.rds

lianos commented 6 years ago

I don't see any mention of an *.rds file in the README with respect to the MSigDB GeneSetDb objects. Can you link specifically to the line you're talking?

All I see in the README that's relevant to MSigDB objects is this bit:

library(multiGSEA)
library(dplyr)
gdb <- getMSigGeneSetDb(c('h', 'c2'), 'human')

... which works. Are we looking in different places, or?

phaverty commented 6 years ago

Yep, that bit fails.

Pete

Peter M. Haverty, Ph.D. Genentech, Inc. phaverty@gene.com

On Wed, Mar 14, 2018 at 2:53 PM, Steve Lianoglou notifications@github.com wrote:

I don't see any mention of an *.rds file in the README with respect to the MSigDB GeneSetDb objects. Can you link specifically to the line you're talking?

All I see in the README that's relevant to MSigDB objects is this bit:

library(multiGSEA) library(dplyr)gdb <- getMSigGeneSetDb(c('h', 'c2'), 'human')

Am I looking in the wrong place, or?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lianos/multiGSEA/issues/2#issuecomment-373187598, or mute the thread https://github.com/notifications/unsubscribe-auth/AH02K22dg8j7jk65qO-LSfYeGKgHuPU1ks5teZFugaJpZM4SOBES .

lianos commented 6 years ago

Have you tried (re-)installing the latest versions?

devtools::install_github("lianos/GeneSetDb.MSigDB.Hsapiens.v61")
devtools::install_github("lianos/GeneSetDb.MSigDB.Mmusculs.v61")

and try again?

Maybe I didn't merge changes from develop to master. If the upstairs commands don't fix it, try to install from develop:

devtools::install_github("lianos/GeneSetDb.MSigDB.Hsapiens.v61", ref = "develop")
devtools::install_github("lianos/GeneSetDb.MSigDB.Mmusculs.v61", ref = "develop")

one of those has to work ...

phaverty commented 6 years ago

I had a fresh install of MSigDB and the two V61 datasets. Installing the V61 datasets from develop did the trick. Thanks!

Pete

Peter M. Haverty, Ph.D. Genentech, Inc. phaverty@gene.com

On Wed, Mar 14, 2018 at 3:24 PM, Steve Lianoglou notifications@github.com wrote:

Have you tried (re-)installing the latest versions?

devtools::install_github("lianos/GeneSetDb.MSigDB.Hsapiens.v61")devtools::install_github("lianos/GeneSetDb.MSigDB.Mmusculs.v61")

and try again?

Maybe I didn't merge changes from develop to master. If the upstairs commands don't fix it, try to install from develop:

devtools::install_github("lianos/GeneSetDb.MSigDB.Hsapiens.v61", ref = "develop")devtools::install_github("lianos/GeneSetDb.MSigDB.Mmusculs.v61", ref = "develop")

one of those has to work ...

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lianos/multiGSEA/issues/2#issuecomment-373195269, or mute the thread https://github.com/notifications/unsubscribe-auth/AH02KynR8MDswnwAp9x5HNQ6hdwBIUCvks5teZingaJpZM4SOBES .

lianos commented 6 years ago

OK, sorry about that ... I've just re-merged the develop branch into master so this two are back to parity for that. Thanks for suffering along with that.