search

matthiasheinig / histoneHMM

Differential peak calling tool for ChIP-seq data
5 stars 1 forks source link

findInterval fails #3

Closed ghost closed 7 years ago

ghost commented 7 years ago

Hi, I am running histoneHMM 1.7 on a BAM file (DEEP project) for H3K9me3 and get the following error:

Error in findInterval(x, quantile(x, prob = (0:ncomp)/ncomp), rightmost.closed = T) : 
  'vec' must be sorted non-decreasingly and not contain NAs
Calls: run.univariate.hmm -> em -> findInterval

Session:

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 7 (wheezy)

locale:
 [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US       
 [4] LC_COLLATE=C         LC_MONETARY=en_US    LC_MESSAGES=en_US   
 [7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C        
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C 

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] histoneHMM_1.7 Rcpp_0.12.8

Best, Peter

ghost commented 7 years ago

Ok, I found the error; it was actually due to a mismatch in chromosome names, closing this now...

matthiasheinig commented 7 years ago

Thanks for following this up!