Open hackkr opened 5 months ago
Hi! Just wanted to follow up with this issue.
Hi! Sorry for the wait. Similarly to sliding_window_chromunity function you should be able to pass in NULL for the genome argument and it should work. Try pulling the latest changes and let me know if it works for you.
Hello,
Sorry my the delayed response! Thanks for working on this issue. I just tried pulling the most recent commits from either the master
or non-standard-genomes-branch
and running my code again, and I am still encountering the same error.
>set.seed(198)
>back_gr = sliding_window_background(chromosome= "NC_017276.1", binsets = sw_this$binsets, resolution = 5e4)
Warning: NAs introduced by coercionGenerating distributions
|==================================================================| 100%, Elapsed 00:01
Generating GRanges
| | 0%, ETA NA
Warning: all scheduled cores encountered errors in user codeError in rbindlist(this.list, fill = TRUE) : Item 1 of input is not a data.frame, data.table or list
traceback:
Error in rbindlist(this.list, fill = TRUE) : Item 1 of input is not a data.frame, data.table or list
2. rbindlist(this.list, fill = TRUE)
1. sliding_window_background(chromosome = "NC_017276.1", binsets = sw_this$binsets, resolution = 50000)
Hello! I am encountering an error when I try to generate background bindsets. I'm wondering if it stems from the use of
hg_seqlengths()
.Here's several work arounds I tried.
I tried supplying a forged a BSgenome for my organism. It is loaded in the environment.
setting genome to NULL as with
sliding_window_chromunity()
in #15 yields a slightly more informative error.setting
DEFAULT_GENOME
to my forged genome does not resolve it. I also tried passing along theseqlengths(Sis_REY15A)
output as a list. Both returned the errorItem 1 of input is not a data.frame, data.table or list