[BioC] GenomeGraphs alternate input
Amanda Miotto
a.miotto at griffith.edu.au
Tue Aug 19 05:54:20 CEST 2008
When trying to alter GenomeGraphs so that it queries a local mysql database
instead of ensembl_mart, I get the following error. Why? What is chunk 4? and
is it due to ens not being classed correctly?
Thankyou.
sudo R --verbose CMD build MyGenomeGraphs
......
* DONE (GenomeGraphs)
* creating vignettes ... ERROR
Loading required package: biomaRt
Loading required package: RCurl
Loading required package: grid
Loading required package: DBI
Error: processing vignette 'GenomeGraphs.Rnw' failed with diagnostics:
chunk 4
Error in ens[i, 5] - ens[i, 4] : non-numeric argument to binary operator
Execution halted
The additional code I included was in GenomeGraphs-classes.R
---------------------------------------------------------------------------------------
#############################################################################################################################
setMethod("initialize", "Gene", function(.Object, ...){
.Object <- callNextMethod()
library(RMySQL)
con <- dbConnect(MySQL(),host="", user="", dbname="", password="")
q1<-("select * from alldata where " )
q3<-("=")
p4<-("'")
.Object at ens<-dbGetQuery(con, paste(q1,.Object at type,q3,p4,.Object at id,p4,
sep=""))
dbDisconnect(con)
# .Object at ens <-
getBM(c("ensembl_gene_id","structure_transcript_stable_id","structure_exon_stable_id",
# "structure_exon_chrom_start","structure_exon_chrom_end","structure_exon_rank",
# "structure_transcript_chrom_strand", "structure_biotype"),
# filters = .Object at type, values=.Object at id,
mart=.Object at biomart)
###########################################################################################################################
-----------------------------------------------------------------------------------------
#############################################################################################################################
if (!is.null(.Object at biomart)) {
library(RMySQL)
con <- dbConnect(MySQL(),host="", user="", dbname="", password="")
q1<-("select * from alldata where structure_transcript_chrom_strand =" )
q3<-("and exon_chrom_start<")
q4<-("and exon_chrom_end>")
q5<-("and structure_strand=")
p4<-("'")
.Object at ens<-dbGetQuery(con,
paste(q1,.Object at chromosome,q3,.Object at start,q4,.Object at end,q5,p4,strand,p4,
sep=""))
dbDisconnect(con)
# .Object at ens <-
getBM(c("ensembl_gene_id","structure_transcript_stable_id",
# "structure_exon_stable_id","structure_exon_chrom_start","structure_exon_chrom_end",
# "structure_exon_rank", "structure_transcript_chrom_strand","structure_biotype"),
#
filters=c("chromosome_name", "start", "end", "strand"),
#
values=list(.Object at chromosome,.Object at start, .Object at end, strand),
# mart=.Object at biomart)
}
############################################################################################################################
------------------------------------------------------------------------------------------------
#########################################################################################################################
library(RMySQL)
con <- dbConnect(MySQL(),host="", user="", dbname="", password="")
q1<-("select * from alldata where " )
q3<-("='")
p4<-("'")
.Object at ens<-dbGetQuery(con, paste(q1,.Object at type,q3,.Object at id,p4, sep=""))
dbDisconnect(con)
# .Object at ens <-
getBM(c("ensembl_gene_id","structure_transcript_stable_id","structure_exon_stable_id",
# "structure_exon_chrom_start","structure_exon_chrom_end","structure_exon_rank",
# "structure_transcript_chrom_strand","structure_biotype"),
# filters = .Object at type,
values=.Object at id,mart=.Object at biomart)
##########################################################################################################################
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