Question: How to make a MotifDb object from pwm/pfm files?
0
gravatar for niuyw
21 months ago by
niuyw0
Beijing, China
niuyw0 wrote:

Hi,

I'm using package MotifDb. It contains thousands motifs of transcription factors from various sources (e.g. JASPAR, CIS-BP etc.), and is very convenient.

My question is: can I create a MotifDb object from pwm/pfm files? Sometimes using motifs not in the package is needed.

Thanks!

Yiwei Niu

 

 

 

 

 

motifdb • 545 views
ADD COMMENTlink modified 21 months ago by Paul Shannon370 • written 21 months ago by niuyw0
Answer: How to make a MotifDb object from pwm/pfm files?
0
gravatar for Paul Shannon
21 months ago by
Paul Shannon370
Paul Shannon370 wrote:

Yiwei,

The process is described in the programmer's guide:

    https://github.com/Bioconductor-mirror/MotifDb/blob/master/vignettes/programmersGuide.txt

The (sometimes) hard part of adding new matrices is obtaining  metadata for each new matrix, and transforming it into the DataTable.  We would be delighted to add new matrices to the package.   Many example scripts for preparing pfms and metadata are included in the package source.

You may also be interested that for the upcoming Bioconductor release, we have added 

  1. JASPAR 2016
  2. HOCOMOCO 10
  3. Homer
  4. SwissRegulon (hg19:FANTOM5)

We also plan to include pwm similarity measures calculated with TOMTOM, from the Meme suite.  

Let us know if we can help.

 - Paul

ADD COMMENTlink written 21 months ago by Paul Shannon370

Sorry for the late reply. It's a good guide! Well, it's difficult for me to obtain all the metadata needed. I'm not familiar with TFs. Very looking forward to the new version of MotifDb.

ADD REPLYlink written 19 months ago by niuyw0
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