Question: TFBSTools access to JASPAR2014 via getMatrixSet()
0
gravatar for JasonLouisStein
4.1 years ago by
United States
JasonLouisStein0 wrote:

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 • 617 views
ADD COMMENTlink modified 4.1 years ago by Ge Tan20 • written 4.1 years ago by JasonLouisStein0
Answer: TFBSTools access to JASPAR2014 via getMatrixSet()
0
gravatar for Ge Tan
4.1 years ago by
Ge Tan20
Switzerland
Ge Tan20 wrote:

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

ADD COMMENTlink written 4.1 years ago by Ge Tan20
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