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)
attached base packages:
 parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
 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
 S4Vectors_0.8.0 BiocGenerics_0.16.0
loaded via a namespace (and not attached):
 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
 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