Reconstruct principal curves from the results of pathifier package
1
0
Entering edit mode
6.9 years ago
arronar ▴ 290

Hello.

I'm using the pathifier tool, to extract PDSs (Pathway de-regulation scores) from some microarray datasets. If someone has already read the paper of this tool, probably he/she has seen the following image of the constructed principal curves.

enter image description here

I search on the internet for a tutorial on how to construct such plots from the results of pathifier, but couldn't find something. As you might know the quantify_pathways_deregulation() returns a curves list but I don't know exactly how to use it.

Does anyone try to re-construct such curve plots from pathifier's results?

Any hint or idea is welcome.

pathway pathifier principal curves bioconductor R • 1.9k views
ADD COMMENT
2
Entering edit mode
6.9 years ago
Suren ▴ 110

Check here .

They shared R codes to do exactly the same. You can also use the produced *RData files to extract the data for constructing the principal curve using scatterplot3d package.

ADD COMMENT

Login before adding your answer.

Traffic: 5713 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6