Hi Taverna users,
I'm trying to use the listq combined table to get mean values for the
methylation, start, end, strand and entrezgene id's. The table file is then
used by another
RShell to make a gene map plot with the mean values. The code gets stuck on
the listq part and gives a lot of the same prints when there is a print
statement
put into the code after listq.
biomart1 and epigen_file are files that are read in R in an earlier RShell.
The R code works without a problem when I try to run it in the
R command-line.
As you can see there is no argument 'x' and there is no function used
that's called 'unique'. I looked at possible fixes in the R mailing lists
but they didn't change
anything and I still got the same error.
As the problem only shows up in Taverna I hope you can help me find out
where the problem is and can help me solve it.
This is the error I get in Taverna:
- Error Trace
- net.sf.taverna.t2.reference.impl.ErrorDocumentImpl@21861ade
- org.rosuda.REngine.Rserve.RserveException: error in evaluating the
argument 'x' in selecting a method for function 'unique': Error: evaluation
nested too deeply: infinite recursion / options(expressions=)?
-
net.sf.taverna.t2.activities.rshell.RshellActivity$1.run(RshellActivity.java:278)
- java.lang.Thread.run(Thread.java:680)
For this code in the RShell:
listq <- cbind(biomart1[as.matrix(ov1)[,1],],
epigen_file[as.matrix(ov1)[,2],])
mean_MRE_values <- aggregate(listq[,15]~listq[,2], data=listq, FUN="mean")
mean_start <- aggregate(listq[,9]~listq[,2], data=listq, FUN="mean")
mean_end <- aggregate(listq[,10]~listq[,2], data=listq, FUN="mean")
strand_uni <- aggregate(listq[,3]~listq[,2], data=listq, FUN="mean")
gene_uni <- aggregate(listq[,1]~listq[,2], data=listq, FUN="mean")
pr_viz_tab <- cbind(mean_start[1], mean_start[,2], mean_end[,2],
strand_uni[,2], gene_uni[,2])
colnames(pr_viz_tab) <- c("name", "start", "end", "strand", "entrezgene",
"MRE_value")
name2 <- paste("vizualization_table_output.tab", sep="")
viz_table_file <- write.table(pr_viz_tab, name2, col.names=TRUE,
row.names=FALSE, sep="\t")
stub <- "stub"
Cheers,
Youri
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