You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I am using polyester package to simulate counts with and without GC bias for 16 samples (8 per group). I am using integers that correspond to Loess models that come with the package. This is how I generated the array:
cg_model<-sample(0:7,16,replace = TRUE)
And then I simulate the experiment:
simulate_experiment('chr22_shuffled.fa', num_reps=c(8,8), reads_per_transcript=basereads, fold_changes=foldm[[1]], outdir='simulated_readswBias', paired = FALSE, gcbias = as.list(cg_model), seed=1234)
And get this error
Error in simulate_experiment("chr22_shuffled.fa", num_reps = c(8, 8), : gc bias parameters must be integers 0 through 7 or loess objects
Parameters are definitely integers. I also tried to enter gcbias as an array to no avail. The code runs beautifully without the gcbias parameter. Any clue as to what is wrong?
Thank you. Any help is appreciated.
The text was updated successfully, but these errors were encountered:
Hi @Aslic, your call to simulate_experiment has this for gcbias: gcbias = as.list(cg_model). The function is expecting a numeric vector, but you are sending it a list. cg_model is already a numeric vector, so you can send it in directly like so: gcbias = cg_model. That should solve your problem, but if you are still getting an error, then come back and explain what you see.
Hi Alyssa,
I am using polyester package to simulate counts with and without GC bias for 16 samples (8 per group). I am using integers that correspond to Loess models that come with the package. This is how I generated the array:
cg_model<-sample(0:7,16,replace = TRUE)
And then I simulate the experiment:
simulate_experiment('chr22_shuffled.fa', num_reps=c(8,8), reads_per_transcript=basereads, fold_changes=foldm[[1]], outdir='simulated_readswBias', paired = FALSE, gcbias = as.list(cg_model), seed=1234)
And get this error
Error in simulate_experiment("chr22_shuffled.fa", num_reps = c(8, 8), : gc bias parameters must be integers 0 through 7 or loess objects
Parameters are definitely integers. I also tried to enter gcbias as an array to no avail. The code runs beautifully without the gcbias parameter. Any clue as to what is wrong?
Thank you. Any help is appreciated.
The text was updated successfully, but these errors were encountered: