listDeByTool: makes a data.frame with genes (lines) and all executed DE tool. Each tool that identify gene as DE, are marked by 1.

Usage

listDeByTool(consexpressionList, geneNames, deList)

Arguments

consexpressionList: A list generated by consexpressionR function
geneNames: name of all genes in experiment (list)
deList: List with names of all genes analysed in experiment

Value

data.frame with genes (lines) and DE tools (column), where 1 shows a DE indication by tool.

Examples

data(gse95077)
treats = c("BM", "JJ")
cons_result <- runExpression(numberReplics = 3, groupName = treats,
                              rDataFrameCount = gse95077,
                              sepCharacter = ",",
                              experimentName = "test_cons",
                              outDirPath = "." )
#> Using classic mode.
#> Getting annotation of the Homo Sapiens...
#> Using reference genome 38.
#> Calculating gene expression values...
#> RQ fit ......
#> SQN 
#> 
#>  
#>  ===== ERROR: KnowSeq execution is failed === 
#>  Error in mclustBIC(data = structure(c(-3.52446659876917, -2.42801002792396, : could not find function "mclustBIC"
#>  
#> Removing intercept from test coefficients
#> 
#>  ------------ limma executed!
#> [1] "Computing (M,D) values..."
#> [1] "Computing probability of differential expression..."
#> 
#>  ------------ NOISeq executed! 
#> Warning: `expect_is()` was deprecated in the 3rd edition.
#> ℹ Use `expect_type()`, `expect_s3_class()`, or `expect_s4_class()` instead
#> Warning: `expect_is()` was deprecated in the 3rd edition.
#> ℹ Use `expect_type()`, `expect_s3_class()`, or `expect_s4_class()` instead
#> Warning: `expect_is()` was deprecated in the 3rd edition.
#> ℹ Use `expect_type()`, `expect_s3_class()`, or `expect_s4_class()` instead
#> Initial number of DE patterns = 2
#> Final number of DE patterns = 2
#> 
#>  ------------ EBSeq executed!
#> 
#>  
#>  ===== ERROR: in DESeq2 execution is failed === 
#>  === Contrast group is: [  ] 
#>  === Control group is: [  ] 
#>  ERROR!! This values are not defined in groupName: [ BM ]
#> 
#>  
#>  ===== ERROR: in DESeq2 execution is failed === 
#>  === Contrast group is: [  ] 
#>  === Control group is: [  ] 
#>  ERROR!! This values are not defined in groupName: [ JJ ]
#> 
#>  ------------ DESeq2 executed!
#> Estimating sequencing depths...
#> Resampling to get new data matrices...
#> perm= 1
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#> Number of thresholds chosen (all possible thresholds) = 8
#> Getting all the cutoffs for the thresholds...
#> Getting number of false positives in the permutation...
#> 
#>  ------------ SAMSeq executed!
#> 
#>  ------------ DIFERENTIAL EXPRESSION ANALYSIS WAS COMPLETE!
expDef_result <- expressionDefinition(resultTool = cons_result, groups = treats)
deByTool <- listDeByTool(consexpressionList = cons_result,
                         geneNames = row.names(gse95077),
                         deList = expDef_result)