[英]How to use bioconductor from rpy2?
I'm trying to use bioconductor (Specifically seqLogo) from rpy2. 我正在尝试从rpy2使用bioconductor(特别是seqLogo)。 I found the helpful package:
我找到了有用的包:
http://pythonhosted.org/rpy2-bioconductor-extensions/index.html http://pythonhosted.org/rpy2-bioconductor-extensions/index.html
however when I try this from the documentation of the package: 但是当我从包的文档中尝试这个时:
import rpy2.robjects as robjects
from rpy2.robjects.packages import importr
base = importr('base')
# evaluate locally a remote R script
base.source("http://www.bioconductor.org/biocLite.R")
base.require("biocLite")
bioclite = robjects.globalenv['biocLite']
I get the error 我收到了错误
File "/usr/local/lib/python2.7/dist-packages/rpy2-2.3.6-py2.7-linux-x86_64.egg/rpy2/robjects/environments.py", line 17, in __getitem__
res = super(Environment, self).__getitem__(item)
LookupError: 'biocLite' not found
In the R environment on my system, the following works perfectly: 在我的系统的R环境中,以下工作完美:
> require(seqLogo)
and I'd like to use this already installed seqLogo
package from rpy2. 我想从rpy2使用这个已安装的
seqLogo
软件包。 How can this be done? 如何才能做到这一点? since I have rpy2 installed, I can do:
因为我安装了rpy2,我可以这样做:
>>> import bioc
but not sure how to install new bioconductor packages like seqLogo from bioc
. 但不确定如何从
bioc
安装新的bioconductor包,如bioc
。
If I try: 如果我尝试:
importr("seqLogo")
I get the error: 我收到错误:
rpy2.rinterface.RRuntimeError: Error in loadNamespace(name) : there is no package called ‘seqLogo’
thanks. 谢谢。
The Bioconductor project changed a bit the internals of its package installer. Bioconductor项目改变了其软件包安装程序的内部结构。 The following should work:
以下应该有效:
from rpy2.robjects.packages import importr
# do the following _only the first time_, to install the package seqLogo
base = importr('base')
base.source("http://www.bioconductor.org/biocLite.R")
biocinstaller = importr("BiocInstaller")
biocinstaller.biocLite("seqLogo")
# load the installed package "seqLogo"
seqlogo = importr("seqLogo")
Otherwise the bioconductor extensions to rpy2 have not been updated for quite some time. 否则rpy2的bioconductor扩展已经有一段时间没有更新了。 There might be other things that would need to be fixed.
可能还有其他事情需要修复。
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