orderMarkers error

[sandr...@gmail.com]

Hello group,

We want to try orderMarkers on all chromosomes except 6, but when we run the following lines of code, we get the error shown below. Any suggestions for moving forward?

Thank you in advance!

> newnot6<-orderMarkers(cross=new, map.function="kosambi", chr=-6,error.prob=0.05, verbose=2)
 - Chr 1
Error in lods[newmar, newmar] : subscript out of bounds
> summaryMap(new)
        n.mar length ave.spacing max.spacing
1         542  220.1         0.4        12.9
2         358  113.8         0.3         6.3
3         501  166.6         0.3         7.4
4         423  197.2         0.5         8.8
5         472  161.0         0.3         8.2
6         568  143.3         0.3         7.1
7         305  153.4         0.5         6.2
8         531  120.8         0.2         8.1
9         367  124.1         0.3        12.5
10        546  186.1         0.3         5.1
11        341  178.4         0.5         9.7
12        428  147.3         0.3        11.7
overall  5382 1912.0         0.4        12.9
> summary(new)
    RI strains via selfing

    No. individuals:    172

    No. phenotypes:     5
    Percent phenotyped: 100 99.4 99.4 96.5 98.3

    No. chromosomes:    12
        Autosomes:      1 2 3 4 5 6 7 8 9 10 11 12

    Total markers:      5382
    No. markers:        542 358 501 423 472 568 305 531 367 546 341 428
    Percent genotyped:  98.1
    Genotypes (%):      AA:49.1  BB:50.9

[Karl Broman]

Maybe try "-6" as a character string rather than an integer? I would think that this notation would work here, so I'm not sure what's wrong.

Alternatively, spell out all of the chromosomes:

newnot6<-orderMarkers(cross=new, map.function="kosambi", chr=c(1:5, 7:12), error.prob=0.05, verbose=2)

karl

[sandr...@gmail.com]

Thank you for the quick response.

I tried both of your suggestions. I also tried just choosing a single chromosome (chr=1 or chr=2). All of these options result in the same error message: Error in lods[newmar, newmar] : subscript out of bounds

[Karl Broman]

This seems to be a problem in reordering the results of est.rf. I've not seen it before and I don't know why it's happening.

Maybe re-run est.rf() before the call to orderMarkers().

  new <- est.rf(new)

karl

On Tuesday, February 16, 2021 at 10:02:56 AM UTC-6  wrote:

Thank you for the quick response.

I tried both of your suggestions. I also tried just choosing a single chromosome (chr=1 or chr=2). All of these options result in the same error message: Error in lods[newmar, newmar] : subscript out of bounds

On Tuesday, February 16, 2021 at 10:22:42 AM UTC-5 wrote:

Maybe try "-6" as a character string rather than an integer? I would think that this notation would work here, so I'm not sure what's wrong.

Alternatively, spell out all of the chromosomes:

newnot6<-orderMarkers(cross=new, map.function="kosambi", chr=c(1:5, 7:12), error.prob=0.05, verbose=2)

karl

[sandr...@gmail.com]

Worked perfectly!

Thank you. I had just reordered and changed the names of the linkage groups to match that of the chromosomes.