[Bioc-devel] Replacing deprecated org.Hs.egCHR and friends

Peter Langfelder peter.langfelder at gmail.com
Tue Jan 13 06:34:05 CET 2015

Hi all,

can anyone please explain or point me to an explanation of how to
replace org.Hs.egCHR and friends that appear to be deprecated in the
devel version? The deprecation message isn't very helpful. Thanks!

x = org.Hs.egCHR
Warning message:
In (function ()  :
  org.Hs.egCHR is deprecated. Please use an appropriate TxDb object or
  package for this kind of data.


R Under development (unstable) (2014-11-24 r67057)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] org.Hs.eg.db_3.0.0    RSQLite_1.0.0         DBI_0.3.1
 [4] AnnotationDbi_1.29.12 GenomeInfoDb_1.3.12   IRanges_2.1.35
 [7] S4Vectors_0.5.16      Biobase_2.27.1        BiocGenerics_0.13.4
[10] BiocInstaller_1.17.3

loaded via a namespace (and not attached):
[1] tools_3.2.0

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