Question: Distance matrix based on mutation rates
gravatar for ceruleanivy
8 months ago by
ceruleanivy30 wrote:

I would like to calculate the phylogenetic distance between 500 patients' breast cancer subtypes and need help when it comes to the right method for producing distance matrices. My patients are equally divided between the 5 sub-types (100 each) and the number of variables represents the number of possible mutated genes and the number of mutations found. Here's an example

       LuminalA  LuminalB  HER2 TNBC
BRCA1  15        45        16   8
KRAS   17        28        6    3
BRAF   19        8         32   28
BCN1   9         15        27   54

I'm currently considering one of PHYLIP's components but I'm open to more viable solutions, so any advice on how to handle the issue is welcome.

ADD COMMENTlink modified 8 months ago by Genebow120 • written 8 months ago by ceruleanivy30
gravatar for Genebow
8 months ago by
Genebow120 wrote:

You may use Pearson coefficient of the distance matrix.

ADD COMMENTlink written 8 months ago by Genebow120
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1365 users visited in the last hour