Entering edit mode
@olegstatberkeleyedu-4310
Last seen 9.6 years ago
Hi, all
I wanted to annotate my peaks using ChIPpeakAnno with a table from
UCSC
genome browser that I was going to import using rtracklayer package.
The
code runs fine if I do this:
library(ChIPpeakAnno)
library(rtracklayer)
session=browserSession()
genome(session)='hg19'
query=ucscTableQuery(session,'refGene')
BUT: if I exchange the order in which I load libraries in a new R
session,
it crashes:
library(rtracklayer)
library(ChIPpeakAnno)
session=browserSession()
genome(session)='hg19'
> query=ucscTableQuery(session,'refGene')
Error in x[[name, exact = FALSE]] :
missing '[[' method for Sequence class GRanges
>
So there seems to be some sort of weird interaction between
ChIPpeakAnno
and rtracklayer that causes errors if ChIPpeakAnno is loaded AFTER
rtracklayer but not before.
It also seems that in general, I need to load ChIPpeakAnno before ANY
OTHER packages I use because for example this works:
library(ChIPpeakAnno)
library(BSgenome.Hsapiens.UCSC.hg19)
library(ShortRead)
library(rtracklayer)
session=browserSession()
genome(session)='hg19'
query=ucscTableQuery(session,'refGene')
but this doesn't:
library(BSgenome.Hsapiens.UCSC.hg19)
library(ChIPpeakAnno)
library(ShortRead)
library(rtracklayer)
session=browserSession()
genome(session)='hg19'
query=ucscTableQuery(session,'refGene')
Error in x[[name, exact = FALSE]] :
missing '[[' method for Sequence class GRanges
Session info for this last session is below. Just letting you know
that
this problem exists.
Oleg.
> sessionInfo()
R version 2.12.0 (2010-10-15)
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=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] rtracklayer_1.9.11 RCurl_1.4-3
[3] bitops_1.0-4.1 ShortRead_1.7.30
[5] Rsamtools_1.1.17 lattice_0.19-13
[7] ChIPpeakAnno_1.5.5 limma_3.5.21
[9] org.Hs.eg.db_2.4.6 GO.db_2.4.5
[11] RSQLite_0.9-2 DBI_0.2-5
[13] AnnotationDbi_1.11.9
BSgenome.Ecoli.NCBI.20080805_1.3.16
[15] multtest_2.5.14 Biobase_2.9.2
[17] biomaRt_2.5.1
BSgenome.Hsapiens.UCSC.hg19_1.3.16
[19] BSgenome_1.17.7 Biostrings_2.17.48
[21] GenomicRanges_1.1.38 IRanges_1.7.39
loaded via a namespace (and not attached):
[1] grid_2.12.0 hwriter_1.2 MASS_7.3-8 splines_2.12.0
[5] survival_2.35-8 XML_3.2-0
>
