Question: Generic functions for DataFrames of Rle objects ?
gravatar for Charles Plessy
19 months ago by
Charles Plessy90 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 19 months ago by Hervé Pagès ♦♦ 13k • written 19 months ago by Charles Plessy90
Answer: A: Generic functions for DataFrames of Rle objects ?
gravatar for Hervé Pagès
19 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,


ADD COMMENTlink written 19 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 17 months ago • written 17 months ago by Charles Plessy90
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 433 users visited in the last hour