[BioC] Reading GFF using Starr

Feseha Abebe-Akele fai4 at cisunix.unh.edu
Wed Mar 2 03:48:38 CET 2011


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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