Moving an allele from one linkage group to another & what to do with extra markers/linkage groups

[Traci Viinanen]

I'm working on constructing a genetic map (the first in this species) - I'm working with ~3000 markers. Rqtl has worked pretty well in grouping them into 21 main linkage groups (the expected number of chromosomes), but there are several markers/groups of a few markers that seem to group with the wrong linkage group.

1. Can I take one or a few markers from one group and 'force' them into another group (perhaps by using the switchAlleles function, but with a single marker)?

2. There are several hundred markers that don't group with anything - well, they very well may, but my thresholds are set fairly strict, max.rf=.35 and min.LOD=30. I've played around with those 2 thresholds, but the linkage groups get very messy and don't make sense, biologically, when I stray from those numbers. Can I somehow delete these extra 'linkage groups'? Or do I just need to re-name a subset of chromosomes...e.g. for the attachment I'm sending you I used: plotRF(mapthis[chr=c(1:21)])

Thanks,
Traci

[Karl Broman]

I also usually start out with strict values for forming linkage groups.

To move markers between linkage groups, use movemarker().

For example, to move marker "rs1341" to linkage group 3, I'd use:

mycross <- movemarker(mycross, "rs1341", 3)

You can move all of the unlinked markers to a linkage group called "un" or something like that.

unlinked <- markernames(mycross, chr=-(1:21)) # markers on chromosomes > 21
for(mar in unlinked)
mycross <- movemarker(mycross, mar, "un")

regards,
karl

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[Traci Viinanen]

Thanks - and how do I switch alleles for a specific marker? Ideally, for a list of specific markers...

[Traci Viinanen]

I thought I could do something like this: 

 mapthis <- switchAlleles(mapthis, markers, switch=c("TP32867", "TP5462", "TP78905", "TP75033", "TP77464", "TP69226", "TP79317", "TP56878"))
Error in match.arg(switch) : 'arg' must be of length 1

obviously not...

On Tuesday, August 20, 2013 2:36:56 PM UTC-5, Traci Viinanen wrote:

[Karl Broman]

switchAlleles() is for fixing genotypes for markers that have their alleles switched.
For example, if AA's are really BB's and vice versa.

karl

[Traci Viinanen]

I think that's what I need to do. I think when I was switching alleles to bring smaller groups of markers into larger linkage groups, some shouldn't have been switched. It's easier to explain if I show you a figure. Here is one of the first markers of linkage group 10:

Again, here are the linkage groups:

I'm pretty sure that the small group from chr 10 belongs in chr 3, but the rf is above .5, so I think I need to switch those alleles, and this may be the case for some other alleles. Thoughts/advice?

Thanks for your help!

Traci

On Tuesday, August 20, 2013 2:36:56 PM UTC-5, Traci Viinanen wrote:

[Karl Broman]

It seems strange that they would get placed on lg 10, if that were the case.

But create a vector named 'markers2fix' with the marker names for that batch on 10 that need to have their alleles switched and be moved to lg 3.

You could switch their alleles with:

mycross <- switchAlleles(mycross, markers2fix)

Then you could try using formLinkageGroups again, or you could move them to lg 3 using a for loop:

for(marker in markers2fix)
mycross <- movemarker(mycross, marker, 10)

karl

On Aug 21, 2013, at 9:44 AM, Traci Viinanen <tvii...@gmail.com> wrote:

> I think that's what I need to do. I think when I was switching alleles to bring smaller groups of markers into larger linkage groups, some shouldn't have been switched. It's easier to explain if I show you a figure. Here is one of the first markers of linkage group 10:
>
>
>

> Again, here are the linkage groups:
>
>

> I'm pretty sure that the small group from chr 10 belongs in chr 3, but the rf is above .5, so I think I need to switch those alleles, and this may be the case for some other alleles. Thoughts/advice?
> Thanks for your help!
> Traci
>
> On Tuesday, August 20, 2013 2:36:56 PM UTC-5, Traci Viinanen wrote:
> I'm working on constructing a genetic map (the first in this species) - I'm working with ~3000 markers. Rqtl has worked pretty well in grouping them into 21 main linkage groups (the expected number of chromosomes), but there are several markers/groups of a few markers that seem to group with the wrong linkage group.
> 1. Can I take one or a few markers from one group and 'force' them into another group (perhaps by using the switchAlleles function, but with a single marker)?
>
> 2. There are several hundred markers that don't group with anything - well, they very well may, but my thresholds are set fairly strict, max.rf=.35 and min.LOD=30. I've played around with those 2 thresholds, but the linkage groups get very messy and don't make sense, biologically, when I stray from those numbers. Can I somehow delete these extra 'linkage groups'? Or do I just need to re-name a subset of chromosomes...e.g. for the attachment I'm sending you I used: plotRF(mapthis[chr=c(1:21)])
>
> Thanks,
> Traci
>
>
>
>