 Dear bioc-sig-sequencing,

I would like to annotate chip-seq peaks for the arabidopsis genome.  I note that GenomicFeatures (section 2.7.3 of the pdf file "Making & using TranscriptDb objects") is suggested for Chip-seq experiments.

Trying the example in section 2.7.3 of the vignette produced the following error message:


> mmusculusEnsembl <-
+    makeTranscriptDbFromBiomart(biomart = "ensembl",
+                                dataset = "mmusculus_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
> rd <- RangedData(ranges = IRanges(start = c(244501,244553,244580,244523),
+                                 end = c(244533,244585,244612,244555)),
+                space = "chr5",
+                strand = "+")
> gr <- as(rd, "GRanges")
> transcriptsByRanges(mmusculusEnsembl, gr, columns=c("tx_id","tx_name","gene_id"))
GRanges with 0 ranges and 2 values columns
> grExt <- gr
> ranges(grExt) <- ranges(grExt)+100
> grExt <- reduce(grExt)
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "reduce", for signature "GRanges"

> sessionInfo()
R version 2.11.0 Under development (unstable) (2010-03-12 r51262)
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_0.4.1 BSgenome_1.15.12      Biostrings_2.15.23
[4] IRanges_1.5.58

loaded via a namespace (and not attached):
[1] Biobase_2.7.5      biomaRt_2.3.4      DBI_0.2-5          RCurl_1.3-1
[5] RSQLite_0.8-4      rtracklayer_1.7.10 tools_2.11.0       XML_2.6-0
>

Thanks,
P. Terry
pterry@huskers.unl.edu

	[[alternative HTML version deleted]]

