Hello, in my code, I need to convert the columns from a robjects.DataFrame to other data types (list, for example). Howver, I've found a problem when dealing with data that contains NAs. In particular, I'm referring to non-numeric columns, that are represented as FactorVectors.
Example code:
import rpy2.robjects as robjects
data = robjects.DataFrame.from_csvfile("file_with_NAs_in_columns", sep="\t")
column_with_na = data.rx2("Column")
print column_with_na
[1] <NA> <NA> <NA> some_value
Levels: some_value
and If I issue
print column_with_na[0]
I get:
-2147483648
And of course, accessing the levels I only get some_value. Converting to other
types of Vector doesn't seem to help.
Notice that this works if I do
base = importr("base")
column_value = base.as_vector(column_with_na)
column_value = list(column_value)
print column_value
['NA', 'NA', 'NA', 'some_value']
Is there a way to translate the column *including* the NAs, into a Python list
without doing the hackish way described above?
This is with RPy 2.1 alpha 2. I admit that there may be a problem with my
installation as I'm running a local copy of rpy2 2.1 as I still have a system-
wide 2.0.x needed for some projects.
--
Luca Beltrame, Ph.D.
Post-doctoral research fellow - Duccio Cavalieri group
Department of Pharmacology, University of Firenze
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