renaming LGs

[Kevin]

This may be a simple thing to do, but I haven't figured out the right
way to do it yet.

I would like to rename my linkage groups. Rather than going from
largest to smallest, the standard in my organism is to label the
chromosome with a sex locus as I and then go from largest to
smallest... Right now I have my sex locus on lg III.


Therefore I would like to change the names on the linkage groups (to
make plotting them easier).


All I can think of is to output the data, change the chromosome IDs in
excel or a text editor and then reimport the data. There must be a
more elegant way than that!

Cheers,
Kevin

[Karl Broman]

A cross object is stored as a list with components "geno" and "pheno". The "geno portion is stored as a list with each component being a chromosome. The chromosome names are defined via the names of those components. You can change the names and order of those as you wish. Consider the following examples, via the 'hyper' data set.

> data(hyper)
> chrnames(hyper)
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10"
[11] "11" "12" "13" "14" "15" "16" "17" "18" "19" "X"
> names(hyper$geno) <- c(19:1, "X")
> chrnames(hyper)
[1] "19" "18" "17" "16" "15" "14" "13" "12" "11" "10"
[11] "9" "8" "7" "6" "5" "4" "3" "2" "1" "X"
> hyper$geno <- hyper$geno[20:1]
> chrnames(hyper)
[1] "X" "1" "2" "3" "4" "5" "6" "7" "8" "9"
[11] "10" "11" "12" "13" "14" "15" "16" "17" "18" "19"

karl

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[BD]

what about scenario like this?

#rename the linkage groups

> names(hyper$geno) <- c(19,17,16,18,15,1:14, "X")
> chrnames(hyper)

[1] "19" "17" "16" "18" "15" "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" [20] "X"

when plotMap again, the linkage groups are arranged in the same order above.

But,how to arrange the linkage groups in order again with the newly assigned id, say [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" [20] "X" ?

Thanks!

[Karl Broman]

hyper$geno is a list, with each component being a chromosome. Changing names(hyper$geno) changes the chromosomes labels. If you want to reorder them, use [ ].

    hyper$geno <- hyper$geno[c(1:19,"X")]

Note that 1:19 will give the vector of numbers 1,2,3,...,19, but when you add "X" to it they will all get converted to the vector of character strings "1", "2", "3", ..., "19", "X". So this will reorder the components according to their names.

Also note that your first bit of code, changing the names, could be made slightly more compact because the : operator can work in either direction.

    names(hyper$geno) <- c(19:15, 1:14, "X")

karl

[BD]

Got it, thank you so much!

[Joshua Havill]

Hi Karl,

I am trying to do something similar (change and sort the names of the linkage groups based upon the physical chromosome they belong to).

The names of the linkage groups were 1 through 10 and ordered based upon size.

chrnames(mapthis.clean) ## Get the names
names(mapthis.clean$geno) <- c(7,8,4,1,2,3,10,9,6,5) ## Change the names based upon the physical chromosome these groups belong too
chrnames(mapthis.clean) ## Check that the names have been changed
mapthis.clean$geno <- mapthis.clean$geno[c(1:10)] ## Sort the groups based upon their names

chrnames(mapthis.clean) ## Check that they've been sorted

Unfortunately, they don't appear to be sorting based upon their names. Any tips?

> chrnames(mapthis.clean)
 [1] "7"  "8"  "4"  "1"  "2"  "3"  "10" "9"  "6"  "5"

[Karl Broman]

Maybe in the reordering step, use character strings to make sure that they get reordered by name and not by numeric index.

So change this line:

    mapthis.clean$geno <- mapthis.clean$geno[c(1:10)] ## Sort the groups based upon their names

To this:

    mapthis.clean$geno <- mapthis.clean$geno[as.character(1:10)]

karl

[havi...@umn.edu]

Thanks Karl!

-------

Joshua Havill

612-836-7834

On Jan 19, 2021, at 6:09 PM, Karl Broman <kbr...@gmail.com> wrote:



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