sequenza2PyClone bug in Sequenza

Question

[hechong]

Dear all

I am currently using Sequenza for tumor cellularity detection.

As pyclone analysis needed, I ran sequenza2PyClone function in R terminal but found following :

"Error: could not find function "sequenza2PyClone"

There is sequenza2Pyclone function in next.R, but could not be called after library(sequenza), with little document about this function.

We are curious about how to use this function

Hoping to hear from you.

;-)

[Govardhan Anande]

Hi Francesco,

I used Sequenza for a project and trying utilise its output to run PyClone. But I am able to find sequenza2pyclone function in recent version (you may have removed as you mentioned in seqeunza user group).

I was wondering, if there is a way to generate input files for PyClone? I am happy to write parser if needed but I am struggling to understand some terminology.

When I tried to correlate sequenza output with the TSV input, I found all the fields except ref and var_counts. Here is the pairing:

pyclone_in_TSV=Sequenza_out_segment 
mutation_id=chr:startposition (optional)
ref_counts= not found 
var_counts=not found
normal_cn=2
minor_cn= B
major_cn=A

Can you please comment on the same and help me generate inputs for the PyClone.

Thanks, Gova

Answer 1

[favero.francesco]

Hi, I've seen this topic only now on Biostars :).

The function is not exported in the namespace because I would not provide an "official" pyClone/sequenza integration, however the function is still accessible from the package:

library(sequenza)
sequenza:::sequenza2PyClone

There is a post about it in the sequenza user group:

https://groups.google.com/forum/#!topic/sequenza-user-group/SPF8v2t1tTc

This will only help you generated the tsv file. You need to manually write the yaml configuration file for pyclone yourself (you can still use sequenza to fill in some parameters such as tumor purity...). And also the function is based on an old version of PyClone, I'm not sure the input format changed since then.

[Govardhan Anande]

Hi Francesco,

I used Sequenza for a project and trying utilise its output to run PyClone. But I am able to find sequenza2pyclone function in recent version (you may have removed as you mentioned in seqeunza user group).

I was wondering, if there is a way to generate input files for PyClone? I am happy to write parser if needed but I am struggling to understand some terminology.

When I tried to correlate sequenza output with the TSV input, I found all the fields except ref and var_counts. Here is the pairing:

pyclone_in_TSV=Sequenza_out_segment 
mutation_id=chr:startposition (optional)
ref_counts= not found 
var_counts=not found
normal_cn=2
minor_cn= B
major_cn=A

Can you please comment on the same and help me generate inputs for the PyClone.

Thanks, Gova