[BioC] chromosome plot

Seth Falcon sfalcon at fhcrc.org
Tue Jun 5 16:19:11 CEST 2007

yanju <yanju at liacs.nl> writes:

> 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")

This isn't enough.  writeChrLengths is, according to its man page,
computing the chromosome lenths based on some source data and writing
an rda file to disk.  You would then need to rebuild the zebrafish
package so that this file becomes part of it.

But I wasn't actually suggesting that you take this route, at least
not initially.

> 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?

I would try simply loading the zebrafishCHRLENGTHS.rda file in your
session and see if that allows buildChromLocation to work -- this is
obviously a temp fix, but an easier first step.

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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