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Question: subset of samples from dba object in DiffBind
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gravatar for ashley.doane
3.0 years ago by
ashley.doane20
United States
ashley.doane20 wrote:

 

Is it possible to create a new dba object based on a subset of the samples in a previous call to dba.count, or dba.analyze?

 

Basically, I would like analyze subsets of samples as seperate analyses, without recounting.  I'm analyzing atac-seq data, which is paired end and >50 million reads per sample for 20-30 samples.  I've been using the summarize overlaps method to count (bSummarizeOverlaps=TRUE), which works great but takes a lot of time even on a server.     

 

A second and related question:  is there a way to pull out a summarizedExperiment from dba.report without limiting to  a specific contrast (or with all contrasts)?  I'm trying to get all of my samples into a summarizedExp object, using the counts and peaks data in the dba object.

 

Thanks for the great package!

Ashley

 

 

 

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by ashley.doane20
2
gravatar for Rory Stark
3.0 years ago by
Rory Stark2.5k
CRUK, Cambridge, UK
Rory Stark2.5k wrote:

Hi Ashley-

The dba() function will let you do both of these things.

Using the supplied tamoxifen resistance dataset as an example:

> data(tamoxifen_counts)
> tamoxifen

You can get a subset of these as a new DBA object:

> responsive <- dba(tamoxifen, mask=tamoxifen$masks$Responsive)
> responsive

You can also use dba() to get a SummarizedExperiment version of the DBA object:

> resp.sumEx <- dba(responsive,bSummarizedExperiment=TRUE)
> resp.sumEx

You could do both of these in one step as well:

> resp.sumEx <- dba(tamoxifen, mask=tamoxifen$masks$Responsive, bSummarizedExperiment=TRUE)

Cheers-

Rory

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Rory Stark2.5k
0
gravatar for ashley.doane
3.0 years ago by
ashley.doane20
United States
ashley.doane20 wrote:

Thanks Rory!

ADD COMMENTlink written 3.0 years ago by ashley.doane20
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