Closed SoniaRuiz closed 5 years ago
juanbot
commented
5 years ago library(CoExpROSMAP) CoExpROSMAP::initDb() tissues <- c("ad","notad") genes <- c("TTLL9","NAGA","RIBC2","NME2","SLC25A34","ZNF470") CoExpNets::reportOnGenesMultipleTissue(tissues=tissues,which.one="CoExpROSMAP",genes=genes)
This should work like that
SoniaRuiz
commented
5 years ago It still returns the same error:
library(CoExpROSMAP) CoExpROSMAP::initDb() Adding 1st net to the DDBBAdding new network probad to the category CoExpROSMAP to the database Adding new network ad to the category CoExpROSMAP to the database Adding new network allsamples to the category CoExpROSMAP to the database tissues <- c("ad","notad") genes <- c("TTLL9","NAGA","RIBC2","NME2","SLC25A34","ZNF470") CoExpNets::reportOnGenesMultipleTissue(tissues=tissues,which.one="CoExpROSMAP",genes=genes) Reading from /home_2/gsit/RLibrary/CoExpROSMAP//extdata/netad.8.it.50.rds Error in readRDS(expr.dataf) : bad 'file' argument
PS: I have reinstalled all packages before testing it again.
juanbot
commented
5 years ago Can you do readRDS("/home_2/gsit/RLibrary/CoExpROSMAP//extdata/netad.8.it.50.rds”) ?
Juan A. Botía Professor in Computer Science and Artificial Intelligence, Universidad de Murcia, Spain Hon. Senior Research Fellow, Institute of Neurology, University College London, UK
On 11 Feb 2019, at 13:22, Sonia Garcia notifications@github.com wrote:
It still returns the same error:
library(CoExpROSMAP) CoExpROSMAP::initDb() Adding 1st net to the DDBBAdding new network probad to the category CoExpROSMAP to the database Adding new network ad to the category CoExpROSMAP to the database Adding new network allsamples to the category CoExpROSMAP to the database tissues <- c("ad","notad") genes <- c("TTLL9","NAGA","RIBC2","NME2","SLC25A34","ZNF470") CoExpNets::reportOnGenesMultipleTissue(tissues=tissues,which.one="CoExpROSMAP",genes=genes) Reading from /home_2/gsit/RLibrary/CoExpROSMAP//extdata/netad.8.it.50.rds Error in readRDS(expr.dataf) : bad 'file' argument
PS: I have reinstalled all packages before testing it again.
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SoniaRuiz
commented
5 years ago Yes, I can:
>library(CoExpNets) >library(CoExpROSMAP) >CoExpROSMAP::initDb() Network notad in category CoExpROSMAP already exists, we can´t overwrite Network probad in category CoExpROSMAP already exists, we can´t overwrite Network ad in category CoExpROSMAP already exists, we can´t overwrite Network allsamples in category CoExpROSMAP already exists, we can´t overwrite >tissues <- c("ad","notad") >genes <- c("TTLL9","NAGA","RIBC2","NME2","SLC25A34","ZNF470") >CoExpNets::reportOnGenesMultipleTissue(tissues=tissues,which.one="CoExpROSMAP",genes=genes) Reading from /home_2/gsit/RLibrary/CoExpROSMAP//extdata/netad.8.it.50.rds Error in readRDS(expr.dataf) : bad 'file' argument >summary(readRDS("/home_2/gsit/RLibrary/CoExpROSMAP//extdata/netad.8.it.50.rds")) Length Class Mode moduleLabels 18167 -none- numeric moduleColors 18167 -none- character MEs 51 data.frame list
juanbot
commented
5 years ago Can you do initDb(mandatory=T) so you rewrite what is in memory?
Juan A. Botía Professor in Computer Science and Artificial Intelligence, Universidad de Murcia, Spain Hon. Senior Research Fellow, Institute of Neurology, University College London, UK
On 11 Feb 2019, at 14:30, Sonia Garcia notifications@github.com wrote:
Yes, I can:
library(CoExpNets) library(CoExpROSMAP) CoExpROSMAP::initDb() Network notad in category CoExpROSMAP already exists, we can´t overwrite Network probad in category CoExpROSMAP already exists, we can´t overwrite Network ad in category CoExpROSMAP already exists, we can´t overwrite Network allsamples in category CoExpROSMAP already exists, we can´t overwrite tissues <- c("ad","notad") genes <- c("TTLL9","NAGA","RIBC2","NME2","SLC25A34","ZNF470") CoExpNets::reportOnGenesMultipleTissue(tissues=tissues,which.one="CoExpROSMAP",genes=genes) Reading from /home_2/gsit/RLibrary/CoExpROSMAP//extdata/netad.8.it.50.rds Error in readRDS(expr.dataf) : bad 'file' argument summary(readRDS("/home_2/gsit/RLibrary/CoExpROSMAP//extdata/netad.8.it.50.rds")) Length Class Mode moduleLabels 18167 -none- numeric moduleColors 18167 -none- character MEs 51 data.frame list
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SoniaRuiz
commented
5 years ago Yes, I can:
>CoExpROSMAP::initDb(mandatory=T) Network notad in category CoExpROSMAP already exists, we can´t overwrite Network probad in category CoExpROSMAP already exists, we can´t overwrite Network ad in category CoExpROSMAP already exists, we can´t overwrite Network allsamples in category CoExpROSMAP already exists, we can´t overwrite >tissues <- c("ad","notad") >genes <- c("TTLL9","NAGA","RIBC2","NME2","SLC25A34","ZNF470") >CoExpNets::reportOnGenesMultipleTissue(tissues=tissues,which.one="CoExpROSMAP",genes=genes) Reading from /home_2/gsit/RLibrary/CoExpROSMAP//extdata/netad.8.it.50.rds Error in readRDS(expr.dataf) : bad 'file' argument >summary(readRDS("/home_2/gsit/RLibrary/CoExpROSMAP//extdata/netad.8.it.50.rds")) Length Class Mode moduleLabels 18167 -none- numeric moduleColors 18167 -none- character MEs 51 data.frame list
juanbot
commented
5 years ago I have discovered the error in findData method in CoExpNets. Would you please update both packages please? Thanks Sonia
SoniaRuiz
commented
5 years ago It works perfectly!! Awesome! Thanks!!
The following error is returned on 'reportOnGenesMultipleTissue' function: