[Bioc-sig-seq] 'agregate' error message
pterry at huskers.unl.edu
pterry at huskers.unl.edu
Wed Dec 23 04:20:58 CET 2009
Dear bioc-sig-sequencing,
I am working with a toy example to learn the material covered in part 3 (Differential expression, pages 10-11) of 'A ChIP-Seq Data Analysis' handout for a 11/19/09 session at the 'High throughput sequence analysis tools and approaches with Bioconductor' workshop in Seattle.
I generated an error message in the following output. Can you comment?
(I note that when I use the sample data & code from the handout, ctcf.rda & gfp.rda, no errors are generated)
> x <- IRanges(start=c(1L, 9L, 4L, 1L, 5L, 10L, 15L, 17L, 17L),
+ width=c(5L, 6L, 3L, 4L, 3L, 3L, 5L, 3L, 3L))
> y <- IRanges(start=c(4L, 4L, 4L, 10L, 10L, 10L),
+ width=c(2L, 2L, 2L, 2L, 2L, 2L))
> cov.x <- coverage(x)
> cov.y <- coverage(y)
> allPeaks <- slice(cov.x, lower = 3)
> allPeaks
Views on a 19-length Rle subject
views:
start end width
[1] 4 5 2 [3 3]
[2] 17 19 3 [3 3 3]
> x.counts <- aggregate(cov.x, allPeaks, sum)
> x.counts
[1] 6 9
> y.counts <- aggregate(cov.y, allPeaks, sum)
Error in findIntervalAndStartFromWidth(start, runLength(x)) :
'x' must be less than 'sum(width)'
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-pc-linux-gnu
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=C 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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChIPseqTutorial_0.0.1 BSgenome.Mmusculus.UCSC.mm9_1.3.16
[3] chipseq_0.2.0 ShortRead_1.4.0
[5] lattice_0.17-26 BSgenome_1.14.0
[7] Biostrings_2.14.1 IRanges_1.4.2
loaded via a namespace (and not attached):
[1] Biobase_2.6.0 grid_2.10.1 hwriter_1.1
>
Thanks,
P. Terry
huskers.unl.edu
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