multiGSEA
multiGSEA copied to clipboard
lianos
Make MSigDB GeneSetDb fetching more robust
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.
The README example fails because it looks for GeneSetDb.MSigDB.Hsapiens-entrez.v61.rds, but has GeneSetDb.MSigDB.Hsapiens.v61.rds
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?
Yep, that bit fails.
Pete
Peter M. Haverty, Ph.D. Genentech, Inc. [email protected]
On Wed, Mar 14, 2018 at 2:53 PM, Steve Lianoglou [email protected] 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 .
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 ...
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. [email protected]
On Wed, Mar 14, 2018 at 3:24 PM, Steve Lianoglou [email protected] 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 .
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.