chromosome plot
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@yanjuliacsnl-1786
Last seen 7.7 years ago
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? Regards, Yanju
zebrafish geneplotter zebrafish geneplotter • 702 views
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.7 years ago
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 -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
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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 > >
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.7 years ago
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 http://bioconductor.org
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