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 seem to be encountering a problem with polyester where an error message reports a discrepancy between the length of the gc bias and the sum of numreps "length(extras$gcbias) == sum(num_reps) is not TRUE", however I can't seem to correct this error as R reports they are indeed equal "length(biases) == sum(num_reps)[1] TRUE".
My commands are:
fastapath = ('/path/to/fastafile') <- has 10 sequences within
numtx = count_transcripts(fastapath) <- [1] 10
transcripts = readDNAStringSet(fastapath) <- "A DNAStringSet instance of length 10"
readmat= matrix(readspertx, nrow=numtx, ncol=10)
set.seed(137)
biases = sample(0:7, 10, replace=TRUE)
readmat_biased = add_gc_bias(readmat, as.list(biases), transcripts)
Hi there,
I seem to be encountering a problem with polyester where an error message reports a discrepancy between the length of the gc bias and the sum of numreps "length(extras$gcbias) == sum(num_reps) is not TRUE", however I can't seem to correct this error as R reports they are indeed equal "length(biases) == sum(num_reps)[1] TRUE".
My commands are:
fastapath = ('/path/to/fastafile') <- has 10 sequences within
numtx = count_transcripts(fastapath) <- [1] 10
transcripts = readDNAStringSet(fastapath) <- "A DNAStringSet instance of length 10"
readmat= matrix(readspertx, nrow=numtx, ncol=10)
set.seed(137)
biases = sample(0:7, 10, replace=TRUE)
readmat_biased = add_gc_bias(readmat, as.list(biases), transcripts)
confirming they're equal:
sum(num_reps) - [1] 10
length(biases) - [1] 10
Then I run
simulate_experiment('/path/to/fastafile', reads_per_transcript=readspertx, num_reps=c(5,5), fold_changes = fold_changes, distr = 'empirical',outdir='bias_gc_sim', gcbias = 'biases')
Which returns the error message "length(extras$gcbias) == sum(num_reps) is not TRUE".
I'd be very grateful into any insight into the issues.
Gill
The text was updated successfully, but these errors were encountered: