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Question: Error in bayespeak function importing data
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gravatar for Reed
3.3 years ago by
Reed10
United States
Reed10 wrote:

I am attempting to use BayesPeak. I have a file of mapped reads from a ChIP-seq experiment and from a negative control in bed6 format. 

The following is my output: 

 

library(BayesPeak)
> raw.output <- bayespeak("chip.bed", "negative.bed", chr = "chr", start = 80000, end = 100000, job.size = 1000)
Read 23148733 records
Read 21898540 records
[0% done] Starting chr:80000-1e+05:Error in var(tr$"+"$norm[x[1]:x[2]]) : 
  error in evaluating the argument 'x' in selecting a method for function 'var': Error in tr$"+"$norm[x[1]:x[2]] : 
  only 0's may be mixed with negative subscripts

I am not sure what is causing this error. Does anyone have some insight into this? I have pasted my session info below.

 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BayesPeak_1.12.0   IRanges_1.20.4     BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] stats4_3.0.2
ADD COMMENTlink written 3.3 years ago by Reed10

Hi - Sorry to hear that. Would you mind posting the top couple of lines from the bed files, so that I can try to reproduce the error? Also, please check that you correctly specified the argument:

chr = "chr"

(This is only correct if you have intentionally made a chromosome called "chr" in your bed file.) Thanks

ADD REPLYlink written 3.3 years ago by Jonathan Cairns10

Thank you for your response. I've supplied the first ten lines from my bed file below. 

chr  0       50      chip_259:H5KJLBCXX:2:2112:14750:28587   255     +
chr  0       50      chip_259:H5KJLBCXX:1:1104:19559:73230   255     +
chr  0       50      chip_259:H5KJLBCXX:2:1214:13540:77997   255     +
chr  0       49      chip_259:H5KJLBCXX:2:2115:5666:26092    255     +
chr  0       49      chip_259:H5KJLBCXX:2:2101:16771:35947   255     +
chr  0       49      chip_259:H5KJLBCXX:2:2111:10107:69803   255     +
chr  0       49      chip_259:H5KJLBCXX:2:2113:20965:92362   255     +
chr  0       49      chip_259:H5KJLBCXX:2:2202:10698:96618   255     +
chr  0       47      chip_259:H5KJLBCXX:2:2105:9883:3050     255     +

 

ADD REPLYlink written 3.3 years ago by Reed10

Hi,

I'm afraid I was unable to reproduce the error. Could you try upgrading to the latest version of R and BayesPeak (I used 3.2.2 and 1.20.0, respectively) please? If you still get the error, try checking that the IRanges object produced by read.bed("chip.bed") makes sense. If this seems OK, then please email me an example of a bed file that causes the error. Thanks!

ADD REPLYlink written 3.3 years ago by Jonathan Cairns10
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