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.
sessionInfo()
R Under development (unstable) (2014-11-24 r67057)
Platform: x86_64-unknown-linux-gnu (64-bit)
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=en_US.UTF-8 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] 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