How to calculate only Modified rogers matrix for 391 genotypes with 1892 markers and export it in csv format?

Gajanan Saykhedkar

unread,

Sep 12, 2019, 12:45:35 AM9/12/19

to Core Hunter Users

Working on a gonotypic data of 391 geno with 1892 markers and trying to calculate modified rogers distance matrix. Can it be done with corehunter?

daveneti

unread,

Sep 12, 2019, 3:38:02 AM9/12/19

to Core Hunter Users

Hi Gajanan,

This should be possible with Corehunter. Have you tried? Are looking to use CH to generate a core subset using MR or just the MR distance matrix. There is other software if you just want to create the distance matrix.

Guy

Gajanan Saykhedkar

unread,

Sep 12, 2019, 3:59:46 AM9/12/19

to Core Hunter Users

Hi daveneti,

Yes I am trying to get MR distance matrix through R script.

Used -

my.data <- genotypes(file = "geno2.csv", format = "biparental")
m <- matrix(runif(782), nrow = 391, ncol = 391)
diag(m) <- 0

but I am not sure that either it is done or not cause both upper diagonal and lower diagonal values are different.

About other software please let know which and will it calculate MR distance matrix?

Thanks

daveneti

unread,

Sep 15, 2019, 1:28:05 AM9/15/19

to Core Hunter Users

Sorry for the late reply. Have you tried https://cran.r-project.org/web/packages/poppr/poppr.pdf

Guy

On Thursday, 12 September 2019 16:45:35 UTC+12, Gajanan Saykhedkar wrote:

Reply all

Reply to author

Forward

Message has been deleted