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Question: Generic functions for DataFrames of Rle objects ?
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gravatar for Charles Plessy
5 months ago by
Japan
Charles Plessy30 wrote:

Dear BioC developers and community,

I am using more and more DataFrames of Rle values, typically for transcriptome expression data, and I end up writing more and more functions that take a DataFrame, lapply a function that unpack the Rle, apply a second function, repack the Rle and convert the resulting list in a DataFrame.  I was just wondering (actually, searched and did not find) if there are already classes or packages providing such a functionality, or provide methods such as colSums, rowsum, cor, etc, adapted to be efficient in that context.

Have a nice day !

ADD COMMENTlink modified 5 months ago by Hervé Pagès ♦♦ 13k • written 5 months ago by Charles Plessy30
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gravatar for Hervé Pagès
5 months ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Hi Charles,

FWIW the DelayedArray package allows you to manipulate a DataFrame of Rle columns as a matrix-like object by just wrapping it inside a DelayedArray object (you do this by calling DelayedArray() on it). See ?DelayedArray for more information. After applying (delayed) operations on it, you can turn the DelayedArray object back into a DataFrame of Rle columns by just coercing it to DataFrame (i.e. with as(  , "DataFrame")). Note that I just added the coercion method to DataFrame in DelayedArray 0.2.5. This new version of the package should become available via biocLite() in 48h or less.

Hope this helps,

H.

ADD COMMENTlink written 5 months ago by Hervé Pagès ♦♦ 13k

Thanks a lot Hervé! It took me some time to understand the obvious, but the DelayedArray wrappers are exactly what I needed.

Would you recommend to I wrap in DelayedArrays just before performing matrix-like operations, or to use the DelayedArray class as the base class for the assays in the SummarizedExperiment objects that I produce ?

(The background of my questions is that I am refactoring the CAGEr package to use MultiAssayExperiments, SummarizedExperiments and DataFrames of Rles extensively).

ADD REPLYlink modified 3 months ago • written 3 months ago by Charles Plessy30
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