[BioC] chromosome plot
yanju at liacs.nl
Tue Jun 5 11:00:45 CEST 2007
I was trying to use writeChrLength in AnnBuilder package like follows:
> path <- file.path(.path.package("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?
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
> + seth
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