Question: Display data summary from R code in my galaxy tool
1
gravatar for Sara Mohammadi
19 months ago by
United States
Sara Mohammadi50 wrote:

I have created a galaxy tool, which get the gene expression data. I want to do some gene expression analysis on this data and display the summary of it. The output file data format which I saved is .tabular.

I do not know how to use this data in the same R code to do and display some statistics summary on it.

Thanks

ADD COMMENTlink written 19 months ago by Sara Mohammadi50

Can you show us your code?

ADD REPLYlink written 19 months ago by Bjoern Gruening5.0k

Thank you so much for your response,

Here is xml wrapper:

 <tool id="get_data" name="Get Study version="0.1.0">
    <description>Get a specific study</description>
     <command detect_errors="exit_code" interpreter="Rscript --vanilla">
        getData.R ${studyid} ${output}
      </command>
      <inputs>
        <param name="studyid" type="select" label="Study ID">
          <option value="SDY269">SDY269</option>
          <option value="SDY270">SDY270</option>
        </param>
      </inputs>
      <outputs>
        <data name="output" format="tabular" label="${studyid}" />
      </outputs>
      <help>
    Obtain a study expression matrix.
      </help>
    </tool>

and R code:

    library(methods)
library(ImmuneSpaceR)
library(Biobase)
library(dplyr)
args = commandArgs(trailingOnly=TRUE)
study.id <- args[1]
out.file <- args[2]
printstudy.id)
print(out.file)
sdy <- CreateConnection(study=study.id)
exprEset <- sdy$getGEMatrix(c("TIV_2008"))
expr <- exprs(exprEset)
print(dim(expr))
probes <- rownames(expr)
saveExpr <- cbind(probes, expr)
colnames(saveExpr) <- c("ProbeID", colnames(expr))
write.table(saveExpr, file=out.file, sep="\t", quote=FALSE, 
              row.names=FALSE, col.names=TRUE) 
    cat("\nSuccess\n")

I want to display the some other information like: dim(), column names, number of samples and other information in the same page as text after getting the data.

Thanks again,

ADD REPLYlink modified 19 months ago • written 19 months ago by Sara Mohammadi50
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