Ununsed Arguement error in cisTopic/TcisTarget

[AAA-3]

Running Code:

date()
pathToFeather <- "/home/ali/Downloads/hg19-regions-9species.all_regions.mc9nr.feather" #deleted after tutorial. file vv large
cisTopicObject <- topicsRcisTarget(object=cisTopicObject, genome='hg19', pathToDb=pathToFeather, reduced_database=FALSE, nesThreshold=3, rocthr=0.005, maxRank=20000)#, nCores=5)
date()

Produces error:

Loading required package: RcisTarget
Error in cisTarget(topicsList[[i]], motifRankings, motifAnnot = motifAnnot,  : 
  unused argument (geneErnMmaxRank = maxRank)

I think there is something wrong with how cisTopic is calling RcisTarget. cisTarget looks for geneErnMaxRank not geneErnMmaxRank.

Is there a way to fix this? I have copied this code directly from the melanoma vignette.

[cbravo93]

Hi!

Yeah I fixed it (we updated the name in RcisTarget but not here a few weeks back), you can reinstall it and try again :)

Thanks!