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Question: chimeraviz - import own fusion file for visualization
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gravatar for verena.tischler
4 months ago by
verena.tischler10 wrote:

Hello,

I would like to use the package "chimeraviz" to visualize fusions.

"chimeraviz allows you to import data from nine different fusion-finders: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPFuse, and STAR-FUSION."

This is information from the "chimeraviz vignette" about how the fusion list is imported

# Load chimeraviz
library(chimeraviz)
# Load SOAPfuse data
if(!exists("soapfuse833ke"))
  soapfuse833ke <- system.file(
    "extdata",
    "soapfuse_833ke_final.Fusion.specific.for.genes",
    package = "chimeraviz")
fusions <- importSoapfuse(soapfuse833ke, "hg38", 10)

I would like to import my own fusion file for visualization but cannot find a way how to import my text file. I would be very grateful for suggestions. Thank you very much!

 

ADD COMMENTlink modified 4 months ago • written 4 months ago by verena.tischler10
1
gravatar for stianlagstad
4 months ago by
stianlagstad70
stianlagstad70 wrote:

Thank you for your interest in using chimeraviz!:) You can use your own file with the import functions like this:

# Load chimeraviz
library(chimeraviz)
# A reference to your fusion file
myfile <- "/home/stian/dev/soapfuse_833ke_final.Fusion.specific.for.genes"
fusions <- importSoapfuse(myfile, "hg38", 10)

See that I've put the path to a fusion file that I have on my disk in the variable "myfile". I use that variable in the import function.

Note that the fusion file has to be from one of the supported fusion finders and you need to use the corresponding import function:
- deFuse -> importDefuse()
- EricScript -> importEricscript()
- InFusion -> importInfusion()
- JAFFA -> importJaffa()
- FusionCatcher -> importFusioncatcher()
- FusionMap -> importFusionmap()
- PRADA -> importPrada()
- SOAPFuse -> importSoapfuse()
- STAR-FUSION -> importStarfusion()

If you have a custom format for your fusion file, then you have to write your own script to import the data into Fusion objects. This isn't very difficult. Take a look at the importDefuse script here and do something similar: https://github.com/stianlagstad/chimeraviz/blob/master/R/importDefuse.R

ADD COMMENTlink modified 4 months ago • written 4 months ago by stianlagstad70
1
gravatar for verena.tischler
4 months ago by
verena.tischler10 wrote:

Thanks a lot Stian for your explanations. I will write my own script for our custom files.

ADD COMMENTlink written 4 months ago by verena.tischler10

No problem! Just ask more here or create an issue in the github repository if there's anything else.

ADD REPLYlink written 4 months ago by stianlagstad70
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