Alex,
No I have not defined he "dataframe" its the spark default Dataframe. That
line is just casting Factor as datarame to send to the function.
Thanks
-R
On Mon, Mar 14, 2016 at 11:58 PM, Alex Kozlov <ale...@gmail.com> wrote:
> This seems to be a very unfortunate name collision. SparkR defines it's
> own DataFrame class which shadows what seems to be your own definition.
>
> Is DataFrame something you define? Can you rename it?
>
> On Mon, Mar 14, 2016 at 10:44 PM, roni <roni.epi...@gmail.com> wrote:
>
>> Hi,
>> I am working with bioinformatics and trying to convert some scripts to
>> sparkR to fit into other spark jobs.
>>
>> I tries a simple example from a bioinf lib and as soon as I start sparkR
>> environment it does not work.
>>
>> code as follows -
>> countData <- matrix(1:100,ncol=4)
>> condition <- factor(c("A","A","B","B"))
>> dds <- DESeqDataSetFromMatrix(countData, DataFrame(condition), ~
>> condition)
>>
>> Works if i dont initialize the sparkR environment.
>> if I do library(SparkR) and sqlContext <- sparkRSQL.init(sc) it gives
>> following error
>>
>> > dds <- DESeqDataSetFromMatrix(countData, as.data.frame(condition), ~
>> condition)
>> Error in DataFrame(colData, row.names = rownames(colData)) :
>> cannot coerce class "data.frame" to a DataFrame
>>
>> I am really stumped. I am not using any spark function , so i would
>> expect it to work as a simple R code.
>> why it does not work?
>>
>> Appreciate the help
>> -R
>>
>>
>
>
> --
> Alex Kozlov
> (408) 507-4987
> (650) 887-2135 efax
> ale...@gmail.com
>
