Getting logR from integer copy number

[beginner984]

Hi

I have minor and total copy number for tumour for my WGS, this is all I have been given as ASCAT output

Is this possible to calculate logR for each segment myself using what I have in my hand?

Thank you so much

[tlesluyes]

Hi,

You should definitely have more output from ASCAT than just copy number solutions. Right after running the ascat.aspcf function, you should get two files per sample: *.BAF.PCFed.txt and *.LogR.PCFed.txt. The latter will contain mean logR values per segment for each probe so here is your logR for each segment. This information is also available in a dedicated data.frame in the ASCAT object (ascat.bc$Tumor_LogR_segmented).

Cheers, Tom.

[beginner984]

Thank you so much

I am working as a data analyst so what I have in my hand from copy number data is like this

> head(cna_data)
  CHROM POS_START  POS_END            Sample Nmaj Nmin ntot   Ploidy
1  chr1     16298 12889922 LP6005334-DNA_H01    2    1    3 2.487561
2  chr1     16298 12889922 LP6005334-DNA_H01    2    1    3 2.487561
3  chr1     16298 12889922 LP6005334-DNA_H01    2    1    3 2.487561
4  chr1     16298 12889922 LP6005334-DNA_H01    2    1    3 2.487561
5  chr1     16298 12889922 LP6005334-DNA_H01    2    1    3 2.487561
6  chr1     16298 12889922 LP6005334-DNA_H01    2    1    3 2.487561
>

I am wondering can I still calculate logR myself based on the what I have?

Or is it safe to put an arbitrary value like 1 for that?

[tlesluyes]

If you only have this information, then there is no way to compute logR on your own. It will just be too hazardous to define several arbitrary values for different copy number solutions.