[Bioc-sig-seq] 'agregate' error message

[pterry at huskers.unl.edu]

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