CoverageView error (bug?)
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termanini ▴ 10
@termanini-8493
Last seen 5.3 years ago

Hi, I would like to use the CoverageView for get the coverage reads of many regions in many samples. I am using the function cov.matrix. 

 

 

 

Since I have many samples and I would like to show the data with an heatmap where each row is a genomic region, each column is a sample and each cell value is the coverage. Therefore, for obtain a single coverage value, I need to set the parameter no_windows=1 instead of, say, 100. In other words, I don't want to slice my genomic region into two or more bins.

However, in this particular case (no_windows=1, offset=0), I get this error:

cov.matrix(covObj, coordfile=my_bed_file, no_windows=1, offset=0, normalization="rpm"); 

[INFO] A coverage matrix composed of average coverages will be generated.

[INFO] processing coords:chr19 1000437 1009723
Error in seq.default(from = (0.9 + bin_width), to = ceil, by = bin_width) : 
  wrong sign in 'by' argument

I think that the code is not capable of manage this particular case where the user don't want to slice regions in bins.

Can anyone help me? Thanks very much!!

----

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

locale:
[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/en_US.UTF-8/it_IT.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] CoverageView_1.6.0   rtracklayer_1.30.1   Rsamtools_1.22.0     Biostrings_2.38.0    XVector_0.10.0       GenomicRanges_1.22.0 GenomeInfoDb_1.6.1   IRanges_2.4.1       
 [9] S4Vectors_0.8.0      BiocGenerics_0.16.0 

loaded via a namespace (and not attached):
 [1] XML_3.98-1.3               GenomicAlignments_1.6.1    bitops_1.0-6               futile.options_1.0.0       zlibbioc_1.16.0            futile.logger_1.4.1       
 [7] BiocParallel_1.4.0         lambda.r_1.1.7             tools_3.2.2                Biobase_2.30.0             RCurl_1.95-4.7             SummarizedExperiment_1.0.0

CoverageView • 652 views
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Hi,

Did you find any solution?

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No, sorry Alberto > Il giorno 16 giu 2017, alle ore 11:37, bioinf [bioc] <noreply@bioconductor.org> ha scritto: > > Activity on a post you are following on support.bioconductor.org > User bioinf wrote Comment: CoverageView error (bug?): > > Hi, > > Did you find any solution? > > Post tags: CoverageView > > You may reply via email or visit C: CoverageView error (bug?)
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