Question: ChIPseeker read count calculation
0
gravatar for c.merce
3.2 years ago by
c.merce0
c.merce0 wrote:

Hello,

I'm interested in using ChIPseeker but there is a point I don't quite understand:
As plotAvgProf() only needs a BED file in order to generate the profile plot, how can you calculate the Read Count Frequency ?
Also, I don't manage to modify the plot aspect, like lines width or color.

Thanks a lot for your help !

chipseeker plotavgprof • 483 views
ADD COMMENTlink modified 3.2 years ago by Guangchuang Yu1.1k • written 3.2 years ago by c.merce0
Answer: ChIPseeker read count calculation
0
gravatar for Guangchuang Yu
3.2 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

pls read the vignette carefully before asking question like this.

The input of plotAvgProf() is definitely not a BED file.

 

ADD COMMENTlink written 3.2 years ago by Guangchuang Yu1.1k

Hello,

Thank you for your reply.

I just realized my mistake checking the content of GEO_sample_data.

Could you please help me with my second issue ? I see that plotAvgProf() is based on ggplot, but I still don't manage to modify my plot, using plotAvgProf() on a tagMatrixList.

Thank you for your time

ADD REPLYlink written 3.2 years ago by c.merce0

hv no idea what 'modify' you want and this is an ggplot2 issue. It would be better to open a new post in stackoverflow or somewhere else.

ADD REPLYlink written 3.2 years ago by Guangchuang Yu1.1k
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