Hello,
I've updated my ShortRead and IRanges packages recently and the qa function
doesn't work for me anymore. It spends a couple of minutes processing, then
fails with an error :
> str(path)
chr "C:/Users/dario/Documents/Garvan/rawData/seq/Ramaciotti/25-03-2010/s_1_1"
> dir(path)
[1] "12627LN-FFPET_MBD2IP_1.Rdata" "12627LN-FFPET_MBD2IP_1.wig.gz"
"12627LN-FFPET_MBD2IP_1_GR.Rdata" "mapping.log"
"s_1_sequence.fastq.gz" "s_1_sequence.uniq.map.gz"
> QAfastq <- qa(path, "fastq.gz", "fastq")
Error in stop(msg, " ", errors, domain = NA) :
no function to return from, jumping to top level
Error in slot(object, ".srlist") :
cannot get a slot (".srlist") from an object of type "NULL"
In addition: Warning message:
UnspecifiedWarning
elements: 1
UnspecifiedError: qa(readFastq(dirPath, pattern, ...), pattern, verbose =
verbose)
error in evaluating the argument 'dirPath' in selecting a method for function
'qa'
> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-pc-mingw32
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.6.2 Rsamtools_1.0.0 lattice_0.18-5
Biostrings_2.16.0 GenomicRanges_1.0.7 IRanges_1.6.15
loaded via a namespace (and not attached):
[1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2 tools_2.11.0
Could this be a bug in the function ?
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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