TFBSTools access to JASPAR2014 via getMatrixSet()
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@jasonlouisstein-7953
Last seen 6.1 years ago
United States

Hello,

When accessing JASPAR2014 database using TFBSTools using the getMatrixSet() function, I see that one needs to set the options of which PWMs to retrieve.  For example

opts[["all_versions"]] <- TRUE
siteList2 <- getMatrixSet(JASPAR2014, opts)

I'm not sure what the option all_versions refers to and I didn't find any information about this in the manual.  In the examples, all_versions is set to TRUE but I'm not sure what this does.  Can someone provide information about this option? 

Thanks very much for your time and help,

Jason

tfbstools jaspar • 759 views
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Ge Tan ▴ 20
@ge-tan-7918
Last seen 3.7 years ago
Switzerland

Hi Jason,

In JASPAR database, we occasionally update the matrices, hence several versions may exist for certain profiles.

Generally, you can just set all_versions=FALSE.

I will update the manual for better clarification.

 

Sorry for the confusion.

Ge

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