Errors when simulating multi-omics data with methylation.

[luyiyun]

I try to simulate a bulk multi-omics data with RNA-seq and Methyl-seq. The code is as follow:

library(MOSim)

omics_list <- c("RNA-seq", "Methyl-seq")
omics_options <- c(
  omicSim("RNA-seq", totalFeatures = 1000),
  # omicSim("miRNA-seq", totalFeatures = 1000)
  omicSim("Methyl-seq", totalFeatures = 2000)
)

set.seed(123)
omics_simulation <- mosim(
  omics = omics_list,
  omicsOptions = omics_options,
  times = 0, numberGroups = 4, numberReps = 100
)

However, I get the following error:

[Pregenerated replicate] Simulating count values for group 4.
error in `[.data.frame`(object@simData, , columnReorder):                                                                                                                                                                                                                   
  undefined columns selected

How can I to solve this error? The version of installed MOSim package is 2.1.1.

[carolinamonzo]

Hi @luyiyun,
I was able to reproduce your error, I've been running some tests and although I'm not exactly sure where the problem is in the MOSim code, I know how to go around it so you can work with it. It seems MOSim is not able to handle 100 replicates per group. If you reduce that (for example, it works fine with 5 replicates), it should run smoothly.
Best,
Carolina.

[luyiyun]

Thanks for your quick reply. If I want to simulate a multi-omics dataset with four groups and 100 samples each group, How can I implement this with MOSim?