I'm learning how to use the BioMM package from Bioconductor just for making some predictions about cancer types based on epigenomic data, but when I follow the tutorial (https://bioconductor.org/packages/devel/bioc/vignettes/BioMM/inst/doc/BioMMtutorial.html) I have a problem with the part of the code that should plot some data: instead of getting the plot I just get an output with this:
posFeature: 50 null device 1
The code I use is exactly the same as the one used in the tutorial:
library(BioMM) library(BiocParallel) library(parallel) library(ranger) library(rms) library(glmnet) library(e1071) library(pROC) library(vioplot) library(variancePartition) library(CMplot) ## Pathway level data or stage-2 data prepared by reconBySupervised() stage2dataA <- readRDS(system.file("extdata", "/stage2dataA.rds", package="BioMM")) head(stage2dataA[, 1:5]) dim(stage2dataA) ### Alternatively, 'stage2dataA' can be created by the following code: ## Parameters classifier <- "randForest" predMode <- "probability" paramlist <- list(ntree=300, nthreads=40) param1 <- MulticoreParam(workers = 1) param2 <- MulticoreParam(workers = 10) set.seed(123) ## This will take a bit longer to run stage2dataA <- reconBySupervised(trainDataList=pathlist, testDataList=NULL, resample="BS", dataMode="allTrain", repeatA=25, repeatB=1, nfolds=10, FSmethod=NULL, cutP=0.1, fdr=NULL, FScore=param1, classifier, predMode, paramlist, innerCore=param2, outFileA=NULL, outFileB=NULL) param <- MulticoreParam(workers = 1) plotVarExplained(data=stage2dataA, posF=TRUE), core=param, horizontal=FALSE, fileName=NULL)
Please, does someone have any idea about what I'm doing wrong or if something is missing?
Thank you so much.