comparison edgeR_Differential_Gene_Expression.xml @ 121:6c90a67a13fa draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc

120:5c94a732bd62

colnames(design_matrix) <- make.names(colnames(design_matrix))

for(i in 1:ncol(design_matrix)) {
  old <- design_matrix[,i]
  design_matrix[,i] <- make.names(design_matrix[,i])
  if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) {
    print("Renaming of factors:")
    print(old)
    print("To:")
    print(design_matrix[,i])
  }
  ## The following line seems to malfunction the script:
  ##design_matrix[,i] <- as.factor(design_matrix[,i])
}

## 1) In the expression matrix, you only want to have the samples described in the design matrix
columns <- match(rownames(design_matrix),colnames(expression_matrix))
columns <- columns[!is.na(columns)]

            <param name="analysis_report_genes" value="significant"/>
            <param name="fdr" value="0.05" />
            
            <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.significant.tabular.txt" />
        </test>
    </tests>
    
    <help>
edgeR: Differential Gene(Expression) Analysis
#############################################

121:6c90a67a13fa

colnames(design_matrix) <- make.names(colnames(design_matrix))

for(i in 1:ncol(design_matrix)) {
  old <- design_matrix[,i]
  
  if(any(grepl("^[0-9]+$", old, perl=TRUE) == FALSE)){
    # Convert invalid names
    design_matrix[,i] <- make.names(design_matrix[,i])
    
    # Print if names have been converted
    if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) {
      print("Renamed of factors:")
      print(old)
      print("To:")
      print(design_matrix[,i])
    }
  } else {
    # Only numerical factors: these are blocking / pairing factors
    design_matrix[,i] <- as.numeric(design_matrix[,i])
  }
}

## 1) In the expression matrix, you only want to have the samples described in the design matrix
columns <- match(rownames(design_matrix),colnames(expression_matrix))
columns <- columns[!is.na(columns)]

            <param name="analysis_report_genes" value="significant"/>
            <param name="fdr" value="0.05" />
            
            <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.significant.tabular.txt" />
        </test>
        <test>
            <param name="analysis_select" value="multi_factor" />
            
            <param name="expression_matrix" value="Differential_Gene_Expression/expression_matrix.tabular.txt" />
            <param name="design_matrix" value="Differential_Gene_Expression/design_matrix.tabular.batch-effects.txt" />
            
            <param name="contrast" value="E-C"/>
        
            <param name="analysis_report_genes" value="all"/>
            <param name="fdr" value="0.01" />
            
            <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.batch-effects.tabular.txt" />
        </test>
    </tests>
    
    <help>
edgeR: Differential Gene(Expression) Analysis
#############################################