Dear Bioc-sig-sequencing,
In lab 8 at BioC2009 on 07/28/09 (Some Basic ChIP-Seq Data Analysis) presented
by D. Sarkar, I would like to be able to get Eland aligned data (from a
*_export.txt file) into a data structure like the 'cstest' data on page 1 of
that handout. This so that I can run an analysis like the poisson distribution
analysis on page 7 of the handout.
I tried the following:
> arabchr1test <- readReads(".", "s_8_export.txt", include = "chr1", simplify =
> TRUE)
Error in validObject(.Object) :
invalid class "SRFilter" object: superclass "ANYTHING" not defined in the
environment of the object's class
> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-11 r49665)
x86_64-unknown-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] GenomicFeatures_0.0.9 chipseq_0.1.26 ShortRead_1.3.34
[4] lattice_0.17-25 BSgenome_1.13.11 Biostrings_2.13.38
[7] IRanges_1.3.79
loaded via a namespace (and not attached):
[1] Biobase_2.5.6 grid_2.10.0 hwriter_1.1
>
Can you comment on how I might successfully proceed?
Thanks,
P. Terry
[email protected]
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