[Bioc-sig-seq] rtracklayer liftOver

Meier, Samuel srm at stowers.org
Wed Dec 8 23:00:13 CET 2010


I am trying to use the liftOver function from the rtracklayer package, but I receive the following error message when attempting to import the chain file downloaded from UCSC.

> import.chain("dm3ToDp3.over.chain")
Error in getClass("Alignment") : "Alignment" is not a defined class

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] rtracklayer_1.10.3
 [2] RCurl_1.4-3
 [3] bitops_1.0-4.1
 [4] BSgenome.Dyakuba.UCSC.droYak2_1.0.0
 [5] BSgenome.Dsimulans.UCSC.droSim1_1.0.0
 [6] BSgenome.Dpseudoobscura.UCSC.dp3_1.0.0
 [7] BSgenome.Derecta.UCSC.droEre1_1.0.0
 [8] BSgenome.Dananassae.UCSC.droAna2_1.0.0
 [9] BSgenome.Dmelanogaster.UCSC.dm3_1.3.16
[10] BSgenome_1.18.0
[11] Biostrings_2.18.0
[12] GenomicRanges_1.2.1
[13] IRanges_1.8.2

loaded via a namespace (and not attached):
[1] Biobase_2.10.0 XML_3.2-0      tools_2.12.0

Sam Meier

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