[BioC] Unable to

[Alex [guest]]

Hi there,

I am new to Galaxy, and would like to create some tools that use some of my existing R scripts. I have played around with the example code, and have found this to be OK, however I am now having problems creating my own tools to use on Galaxy. My interest is in a user being able to upload a gene expression dataset, and then be able to carry out some functions using Galaxy for gene regulatory network inference and analysis.

The first simple tool that I would like to create is a correlation matrix from a gene expression dataset that the user uploads to Galaxy. I have created the .Rd file, called corMat.Rd,which is as follows:

\name{corMat}
\alias{corMat}
\title{a corMat function}
\usage{
  corMat(inputfile = GalaxyInputFile(), 
    outputfile = GalaxyOutput("mydata"," csv"))
}
\arguments{
  \item{input}{An input dataset}

  \item{output}{the output}
}
\description{
  A correlation matrix function
}
\details{
  nothing
}


I then defined the corMat function in R, which is as follows:

corMat <- function (inputfile = GalaxyInputFile(),
outputfile = GalaxyOutput("mydata", "csv")) 
{
    data1 <- tryCatch({
        as.matrix(read.delim(inputfile1, row.names = 1))
    }, error = function(err) {
        stop("failed to read first data file: ", conditionMessage(err))
    })
    
    data2 <- cor(data1)
    write.csv(data2, file = outputfile)
}

To carry this out, I wish to use the cor function in the package WGCNA, so I then have put the following code into R:

galaxy(
corMat,
manpage="/home/adminuser/galaxy-dist/tools/Network/corMat.Rd",
package="WGCNA",
is.exported="TRUE",
version="0.1",
name="Correlation Matrix",
galaxyConfig=GalaxyConfig(
galaxyHome=path.expand("~/galaxy-dist"),
toolDir="tools/Network",
sectionName="Network",
sectionId="NetworkId")
)

However, this does not compile, and gives me the error message:

Error in newXMLTextNode(title) : 
  CHAR() can only be applied to a 'CHARSXP', not a 'NULL'

This error seems to occur when I change the name of the package from RGalaxy to anything else, however I need to change this to WGCNA to specify where to find the function cor that I use in the corMat function I have written for Galaxy. I am obviously making a mistake somewhere, however I cannot see where this error is. Would you be able to help me with this? I can see the power of having a web based user interface that can carry out powerful and intensive biomedical applications in an easy to use format, so am keen to get this to work.


Kind regards,

Alex

 -- output of sessionInfo(): 

R version 2.14.1 (2011-12-22)
Platform: i686-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] parallel  splines   tools     stats     graphics  grDevices
 [7] utils     datasets  methods   base     

other attached packages:
 [1] WGCNA_1.25-2        doParallel_1.0.1    iterators_1.0.6    
 [4] foreach_1.4.0       MASS_7.3-16         reshape_0.8.4      
 [7] plyr_1.8            cluster_1.14.1      Hmisc_3.10-1       
[10] survival_2.36-10    flashClust_1.01-2   dynamicTreeCut_1.21
[13] impute_1.28.0       RGalaxy_1.0.0       digest_0.6.3       
[16] optparse_1.0.1      XML_3.95-0.1       

loaded via a namespace (and not attached):
[1] Biobase_2.14.0     BiocGenerics_0.4.0 brew_1.0-6        
[4] codetools_0.2-8    getopt_1.19.0      grid_2.14.1       
[7] lattice_0.20-0     roxygen2_2.2.2     stringr_0.6.2  

--
Sent via the guest posting facility at bioconductor.org.