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

[pterry at huskers.unl.edu]

Dear bioc-sig-sequencing,

I am trying to analyze Eland aligned files for differential expression, using the 'A ChIP-Seq Data Analysis' handout from 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?

...

> alns_8 <- readAligned(cdataDir, pattern, "SolexaExport")
> alns_8
class: AlignedRead
length: 1380439 reads; width: 35 cycles
chromosome: chr1.fas chr1.fas ... chr1.fas chr1.fas
position: 7568294 167488 ... 4687256 5376960
strand: + + ... + +
alignQuality: NumericQuality
alignData varLabels: run lane ... filtering contig
> head(sread(alns_8))
  A DNAStringSet instance of length 6
    width seq
[1]    35 AGCTATGATCAAGAGAACCTTTCACGATCANNNCN
[2]    35 CGGACGACGGGTAGTTTCGGGCTGTACCAANNNAN
[3]    35 AGCTCAGCGATCTGAGCCACTTGCTCTTTGNNNTN
[4]    35 GGGCCATAGGCCCGTTAAAATATTTTTCTCTNNCT
[5]    35 ATTGTCCATTGACAAATGAAGATATTGGGATNNTT
[6]    35 ACCCCTCCACCAGTATGTTGGCGAAAATCTCNNCC
> table(strand(alns_8), useNA="ifany")

     -      +      *
689912 690527      0

...

> library(BSgenome.Athaliana.TAIR.04232008)
> arab.chromlens <- seqlengths(Athaliana)
> head(arab.chromlens)
    chr1     chr2     chr3     chr4     chr5     chrC
30432563 19705359 23470805 18585042 26992728   154478
> cov.arab8 <- coverage(alns_8, width = arab.chromlens, extend = 126L)
Error: UserArgumentMismatch
  'names(width)' (or 'names(end)') mismatch with 'levels(chromosome(x))'
  see ?"AlignedRead-class"

> 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] BSgenome.Athaliana.TAIR.04232008_1.3.16
[2] chipseq_0.2.0
[3] ShortRead_1.4.0
[4] lattice_0.17-26
[5] BSgenome_1.14.0
[6] Biostrings_2.14.1
[7] 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
pterry at huskers.unl.edu