[BioC] Reading GFF using Starr

[Wolfgang Huber]

Dear Feseha

I am not sure whether this will solve your question, but have you tried

cat chrI.gff chrII.gff chrIII.gff chrIV.gff chrV.gff chrX.gff > all.gff

(on the OS command line) and then

transcriptAnno = read.gffAnno("all.gff", feature="transcript")

(in R). Alternatively, if you are so unfortunate to work with an 
operating system that does not have 'cat', you could also e.g. use R's 
readLines and writeLines.

	Best wishes
	Wolfgang
	


Il Mar/2/11 3:48 AM, Feseha Abebe-Akele ha scritto:
> Hello everyone;
> I am trying to analyze Tiling array data using Starr Package
> and I am stuck at reading GFF files for the 7 genomic sequences
> of C. elegans. In the example that come with the vignette, a
> single primordial gff file (20 lines?) is used whic is not
> anywhere near the 56 MN (combined) gff files.
>
> My question is: how do I read in multiple gff files for analysis?
> among other things I have tried reading them like:
>
> gffs <- c(file.path(dataPath,"chrI.gff"),
> file.path(dataPath,"chrII.gff"), file.path(dataPath,"chrIII.gff"),
> file.path(dataPath,"chrIV.gff"), file.path(dataPath,"chrV.gff"),
> file.path(dataPath,"chrX.gff"))
>
> transcriptAnno <- read.gffAnno(gffs, feature="transcript")
>
> But none worked for me.
>
> I would appreciate any help in getting my analysis to the next level:
>
> FYI:
> I am trying to analyze TEST vs CONTROL experession differential
> on the C. elegans Tiling Array 1.0 chips.
>
> Thanks
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber