RPy2 和 Bioconductor：基因表达示例

Question

我正在尝试弄清楚如何在 Bioconductor 中进行经典基因表达示例使用 Rpy2，我一开始就陷入困境。你如何加载数据？在 R 中，我们这样做：

> library('ALL')
> library('limma')
> data('ALL')

在 Python 中，我们这样做：

>>> import rpy2.robjects as robjects
>>> from rpy2.robjects.packages import importr
>>> base = importr('base')
>>> ALL = importr('ALL')

如何执行与以下内容等效的 Python：

> data('ALL') ??

我没有看到在扩展的文档中加载包数据的示例。我认为这可能是这样，但似乎数据不属于正确的类别，因为当输入到 featureNames 时，它具有 signature“character”：

>>> data = robjects.r('data(ALL)')
>>> data.rclass
<rpy2.rinterface.SexpVector - Python:0x1004b3828 / R:0x10376d558>
>>> featureNames = robjects.r('featureNames')
>>> featureNames(data)
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "featureNames", for signature "character"
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Python/2.6/site-packages/rpy2-2.2.2dev_20110818-py2.6-macosx-10.6-universal.egg/rpy2/robjects/functions.py", line 82, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/Library/Python/2.6/site-packages/rpy2-2.2.2dev_20110818-py2.6-macosx-10.6-universal.egg/rpy2/robjects/functions.py", line 34, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "featureNames", for signature "character"

更新：我想我有它现在：

>>> import rpy2.robjects as robjects
>>> from rpy2.robjects.packages import importr
>>> base =  importr('base')
>>> ALL = importr('ALL')
>>> data = robjects.r('data(ALL)')
>>> data.rclass
<rpy2.rinterface.SexpVector - Python:0x258b190 / R:0xdf86c8>
>>> data = robjects.globalenv['ALL']
>>> data
<RS4 - Python:0x2591490 / R:0x29a2134>
>>> data.rclass
<rpy2.rinterface.SexpVector - Python:0x258b3b0 / R:0xdf85c8>
>>> featureNames = robjects.r('featureNames')
>>> featureNames(data)
<StrVector - Python:0x23e4f08 / R:0x304fc00>
['1000..., '1001..., '1002..., ..., 'AFFX..., 'AFFX..., 'AFFX...]
>>> exprs = robjects.r['exprs']
>>> e = exprs(data)
>>> e
<Matrix - Python:0x23b2da0 / R:0x84d8000>
[7.597323, 5.046194, 3.900466, ..., 3.095670, 3.342961, 3.842535]
>>> 

Answer 1

这个问题应该在包含rpy2的bioconductor扩展的Python包中解决