Warning message: Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.

[yuanyuan chen]

Hi Dr. Broman,

I have one problem about the warning message :

Warning message:

In summary.cross(KNC) :

  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.

  (Perhaps it is in basepairs?)

When I tried to construct the linkage map, at "orderMarkers", the programming always got the error:

 Error in ripple(cross, chr = 1, window = window, verbose = FALSE) : 

  could not find function "testchr" 

4  ripple(cross, chr = 1, window = window, verbose = FALSE) 

3  summary(ripple(cross, chr = 1, window = window, verbose = FALSE)) 

2  orderMarkers.sub(cross, i, window = window, use.ripple = use.ripple, 

    verbose = verbose.sub) 

1  orderMarkers(KNC, chr = 1, maxit = 1000, map.function = "kosambi", 

    sex.sp = F, verbose = T)

Right now I found the bug, use"qtl:::testchr" instead of "!testchr" in your original script. 

But I have another error, saying that "Chr1 not found".  I don't know it is because the length(chr) >1 that ripple stop. 

What shall I do right now? Can you give me some suggestion? 

Thank you!

Sincerely,

Chen

[Karl Broman]

The warning about ">1000 cM" can be ignored.

I still don't understand the problem with ripple and "testchr". Within the R/qtl package, I shouldn't need to use qtl:::testchr.

Please provide more complete context of the problem: what code are you using? What script are you referring to?

karl

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[yuanyuan chen]

Hi Dr. Broman,

I can give you the copy of Console I got. Here is the error information. Another file is my script. Please help me to overcome it. Thanks a lot, I really appreciate your time!

[Karl Broman]

I don't understand your need for the file "DO THIS BEFORE YOU ANALYZE MARKER ORDER.R" because these functions are part of R/qtl. And this is what is causing your problems, as they refer to internal R/qtl functions such as that testchr() function.

Perhaps the functions in the "DO THIS BEFORE..." file have been modified from those in R/qtl? But in this case, you need to include qtl::: with every internal R/qtl function.

karl

> On Mar 25, 2016, at 2:08 PM, yuanyuan chen <yych...@gmail.com> wrote:
>
>
> Hi Dr. Broman,
>

> Here I attached the script I use and my data. I also upload your original script in which I edit "qtl:::testchr" and the copy of Console I got.
> I really don't know how to fix it. Please help me! I really appreciate your time!

>
>
>
> On Friday, March 25, 2016 at 12:43:29 PM UTC-5, Karl Broman wrote:

> <Ki3NC356 script><Ki3NC356_3_rot.csv><DO THIS BEFORE YOU ANALYZE MARKER ORDER.R><Console.docx>

[yuanyuan chen]

Hi Dr. Broman,

In the file"DO THIS BEFORE YOU ANALYZE MARKER ORDER.R" I just edit "setTXTprogressbar" in each function, so that I can see the progress of each function. 

Have you run my data? You suggestion is that I don't need  the file"DO THIS BEFORE YOU ANALYZE MARKER ORDER.R" before I run my map-construction script, right? 

I tried to run the script directly before, the programming was running without stop. I didn't know what's going on. So I thought to add progressbar.

Thank you so much. I will try again, skip the file"DO THIS BEFORE YOU ANALYZE MARKER ORDER.R" 

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