Renaming linkage groups (map construction)?

[Maunveri]

Hello again,

I am trying to re-construct a genetic map of a wheat bi-parental mapping population using a combination of the qtl and ASMap packages.

(side note: the original map has 31 linkage groups named "1" to "31", but wheat only has 21 chromosomes so I want to improve it for later QTL analyses)

Once I am satisfied with my linkage groups, is there a simple way to rename them from the default into something useful (e.g. from "L.10" into "5D")? 

It would be much easier for later analyses than having a random L. number from 1 to 21.

I already renamed some groups whilst using splitCross() and mergeCross() functions (ASMap); however e.g. mergeCross doesn't enable renaming by entering just one group as an argument (hard to merge a single group, I agree... but worth a try ;) ).

Thanks in advance,

Marie

[Karl Broman]

You can change the names of the chromosomes by assigning a vector of character strings to names(mycross$geno)

For example:

data(hyper)

chrnames(hyper) # gives numbers 1-19 and then X

names(hyper$geno) <- c("one", "two", "three", "four", "five", "six", "seven", "eight", "nine", "ten", 

                       "eleven", "twelve", "thirteen", "fourteen", "fifteen", "sixteen", "seventeen", "eighteen", "nineteen", "X")

chrnames(hyper)

karl