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gcbias argument in simulate experiment #55
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Hi @Aslic, your call to |
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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.
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