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juanbot / CoExpNets

Co-expression network management based on WGCNA + k-means
Apache License 2.0
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generateModuleTOMs() error #18

Closed SoniaRuiz closed 4 years ago

SoniaRuiz commented 4 years ago

Hi Juan,

After re-installing CoExpNets, CoExpROSMAP and GTEx packages, I have tried to make a request to the method 'generateModuleTOMs()'. However, I have received this error:

generateModuleTOMs(out.path="my_preferred_path") Working on AdiposeSub Reading from /home_2/gsit/RLibrary/CoExpGTEx//gtexv6/netAdiposeSub.17.it.50.rds Reading from /home_2/gsit/RLibrary/CoExpGTEx//gtexv6/netAdiposeSub.17.it.50.rds Creating TOM for 19282 genes and 350 samples, beta 17 and type signed Error in adjacency(expr.data, power = beta, type = net.type) : no se pudo encontrar la función "adjacency"

Am I doing something wrong? Below, all steps I have followed prior calling the indicated method:

remove.packages('CoExpNets') remove.packages('CoExpROSMAP') remove.packages('CoExpGTEx')

install_github('juanbot/CoExpNets', force=T) install_github('juanbot/CoExpROSMAP', force=T) install_github('juanbot/CoExpGTEx', force=T)

library(CoExpNets) library(CoExpROSMAP) library(CoExpGTEx) library(CoExp10UKBEC) library(CoExpGTExV7) CoExpROSMAP::initDb(mandatory=T) CoExpGTEx::initDb(mandatory=T) CoExp10UKBEC::initDb(mandatory=T) CoExpGTExV7::initDb(mandatory=T) CoExpNABEC::initDb(mandatory=T)

generateModuleTOMs(out.path="my_path")

Regards, Sonia

SoniaRuiz commented 4 years ago

Close this issue as it is already solved.