Problems with Interaction plot

[nata...@gmail.com]

Hi,

I'm using the effectplot() with 2 markers and there's something wrong with the graph.

for example:

Here's the data:

$BDM2$Means

                  201323.AA 201323.AB  201323.BB

51714.AA 0.3368516 0.8748651 0.00000000

51714.AB 0.0000000 0.2424017 0.00000000

51714.BB 0.0000000 0.2773551 0.06912045

$BDM2$SEs

                   201323.AA  201323.AB  201323.BB

51714.AA 0.06789491 0.13684382 0.38972611

51714.AB 0.18725105 0.05095344 0.12252230

51714.BB 0.38629296 0.14511003 0.07196057

Thanks a lot,

Nataly

[Karl Broman]

The line segments missing from the graph indicate that there are no individuals with the double-recombinant (AA,BB) and (BB,AA) genotypes.

But I would expect that the output would have NA for those values, such as in the example below, where the (AA,BB) genotype is absent.

karl

set.seed(20210729)

library(qtl)

data(fake.f2)

fake.f2 <- sim.geno(fake.f2, n.draws=128, step=1)

(out_effplot <- effectplot(fake.f2, mname1="1@5", mname2="1@7"))
$Means
         1...@7.0.AA 1...@7.0.AB 1...@7.0.BB
1...@5.0.AA 21.44141 20.17869       NA
1...@5.0.AB 22.67253 24.56918 18.60580
1...@5.0.BB 17.75186 22.19160 25.44724

$SEs
          1...@7.0.AA  1...@7.0.AB  1...@7.0.BB
1...@5.0.AA 0.6455828 4.4105666        NA
1...@5.0.AB 5.4346461 0.5265628 9.3071026
1...@5.0.BB 4.5490475 6.8012948 0.7549752

[nata...@gmail.com]

Thanks

It happened only when both markers are on the same chr

and as you mentioned, the second one has NA:

$FOB3_bin$Means

         121157.AA    121157.AB 121157.BB

26868.AA 0.5416667 0.0003090243        NA

26868.AB 1.0000000 0.6028191068 1.0000000

26868.BB        NA 0.0000000000 0.1363636

$FOB3_bin$SEs

         121157.AA  121157.AB  121157.BB

26868.AA 0.09080416 0.25694735         NA

26868.AB 0.31455483 0.05714834 0.31455483

26868.BB         NA 0.23790311 0.09484185

If I have the values as in my first example, how can I fix the graph?

ב-יום חמישי, 29 ביולי 2021 בשעה 15:42:55 UTC+3, ‪Karl Broman‬‏ כתב/ה:

[Karl Broman]

I don't think I have a good answer to your question, "If I have the values as in my first example, how can I fix the graph?"

If you have values as in the first example (with no NAs), than I think they all should be shown in the graph. If there are NAs in the results, it is because those genotypes are unobserved, and I don't think there's a solution for that.

karl

[nata...@gmail.com]

I had a mistake, 

found it.

thanks a lot!

Nataly

ב-יום חמישי, 29 ביולי 2021 בשעה 21:12:32 UTC+3, ‪Karl Broman‬‏ כתב/ה: