problem with ggbio
0
0
Entering edit mode
skm770 • 0
@skm770-6777
Last seen 7.0 years ago
United States

HiĀ 

I was wondering if any of you has used "ggbio" before. I was going through its manual and for some of the examples I can not make it work with certain genes. In my case I was trying to use it with "PTPN11" gene using the following code.

library(ggbio)
library(GenomicRanges)
library(BSgenome.Hsapiens.UCSC.hg19)
library(biovizBase)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(VariantAnnotation)
library(Homo.sapiens)

data(genesymbol, package = "biovizBase")

wh <- genesymbol['PTPN11']

p.txdb <- autoplot(Homo.sapiens, which = wh)

It throws the following error

"gap" is not matching to following arbitrary model terms"cds CDS Cds exon EXON Exon utr UTR Utr"

Constructing graphics...
Error in `[[<-`(`*tmp*`, name, value = 1L) 
 1 elements in value to replace 0 elements
Calls: apply ...  -> .local -> .hackFun -> $<- -> $<- -> [[<- -> [[<-
Execution halted

In some forums I have found that installing new version of ggbio could solve the problem. But I am unable to do so using :-

library(BiocInstaller)
useDevel()

or downloading the svn repository using svn checkout tarring it and installing it using R CMD INSTALL.

This is the graph that gets generated using full code that I have. It works for certain genes and not for others.

https://drive.google.com/file/d/0B9g-QPZ8EqmUMjJzRElTTWZIaGM/edit?usp=sharing

I was wondering if somebody has dealt with this ggbio problem before and suggest possible solutions regarding the same.

Also if there is a better way to do the same.

Thanks

ggbio software error homo.sapiens PTPN11 • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 247 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6