[BioC] chromosome plot

[yanju]

Hello Seth,

I was trying to use writeChrLength in AnnBuilder package like follows:

 > library("annotate")
 > library("geneplotter")
 > library("AnnBuilder")
 > library(zebrafish)
 > path <- file.path(.path.package("zebrafish"))
 > writeChrLength("zebrafish","/usr/local/lib/R/site-library/", 
zebrafishCHRLENGTHS)
 > new<-buildChromLocation("zebrafish")

But still I got the error:
Error in get(x, envir, mode, inherits) : variable "zebrafishCHRLENGTHS" 
was not found

my zebrafishCHRLENGTHS variable is the same type as hgu95av2CHRLENGTHS. 
and there is a zebrafishCHRLENGTHS.rda file in 
/usr/local/lib/R/site-library/zebrafish/data directory after 
writeChrLength command. What is wrong?

Regards,
Yanju


Seth Falcon wrote:
> yanju <yanju at liacs.nl> writes:
>
>   
>> Dear all,
>>
>> I was trying to visualize genes in each chromosomes in Zebrafish. I 
>> found how people visualize them in Human species using geneplotter. Then 
>> I tried followings:
>>
>>  > library("annotate")
>>  > library("geneplotter")
>>  > library(zebrafish)
>>  > newChrom<-buildChromLocation("zebrafish")
>>
>> then I got a error:
>> Error in get(x, envir, mode, inherits) : variable "zebrafishCHRLENGTHS" 
>> was not found
>>
>> There is no zebrafishCHRLENGTHS variable which record the length of each 
>> chromosome in Zebrafish. What should I do?
>>     
>
> At present, AnnBuilder only produces the CHRLENGTHS map for humna,
> mouse, and rat platforms.  We hope to increase the coverage in the
> next release.  One solution would be to use the UCSC Genome Browser to
> determine the lengths and create a map object with the appropriate
> name.
>
> + seth
>
>