Sort rows in a MTD matrix to match the expected order

Helper function to sort a mzTab-M MTD matrix, such as generated by mtdSkeleton(), into the correct order of the metadata fields.

Usage

mtdSort(x)

Arguments

x

two-column matrix with the first column containing the metadata field names.

Value

input parameter x sorted into the correct order.

See also

MTD-export for other functions defining metadata information

Author

Johannes Rainer

Examples

## Minimal MTD section
mtd <- mtdSkeleton(id = "001", software = "[MS, MS:1001582, xmcs, 4.0.0]")

mtdSort(mtd)
#>       [,1]                                        
#>  [1,] "mzTab-version"                             
#>  [2,] "mzTab-ID"                                  
#>  [3,] "mzTab-profile"                             
#>  [4,] "software[1]"                               
#>  [5,] "quantification_method"                     
#>  [6,] "cv[1]-label"                               
#>  [7,] "cv[1]-full_name"                           
#>  [8,] "cv[1]-version"                             
#>  [9,] "cv[1]-uri"                                 
#> [10,] "cv[2]-label"                               
#> [11,] "cv[2]-full_name"                           
#> [12,] "cv[2]-version"                             
#> [13,] "cv[2]-uri"                                 
#> [14,] "cv[3]-label"                               
#> [15,] "cv[3]-full_name"                           
#> [16,] "cv[3]-version"                             
#> [17,] "cv[3]-uri"                                 
#> [18,] "database[1]"                               
#> [19,] "database[1]-prefix"                        
#> [20,] "database[1]-version"                       
#> [21,] "database[1]-uri"                           
#> [22,] "small_molecule-quantification_unit"        
#> [23,] "small_molecule_feature-quantification_unit"
#> [24,] "small_molecule-identification_reliability" 
#>       [,2]                                                                     
#>  [1,] "2.1.0-M"                                                                
#>  [2,] "001"                                                                    
#>  [3,] "M"                                                                      
#>  [4,] "[MS, MS:1001582, xmcs, 4.0.0]"                                          
#>  [5,] "[MS, MS:1001834, LC-MS label-free quantitation analysis, ]"             
#>  [6,] "MS"                                                                     
#>  [7,] "PSI-MS controlled vocabulary"                                           
#>  [8,] "4.1.138"                                                                
#>  [9,] "https://www.ebi.ac.uk/ols4/ontologies/ms"                               
#> [10,] "PRIDE"                                                                  
#> [11,] "PRIDE PRoteomics IDEntifications (PRIDE) database controlled vocabulary"
#> [12,] "16:10:2023 11:38"                                                       
#> [13,] "https://www.ebi.ac.uk/ols/ontologies/pride"                             
#> [14,] "STATO"                                                                  
#> [15,] "General purpose STATistics Ontology"                                    
#> [16,] "2026-04-20"                                                             
#> [17,] "https://www.ebi.ac.uk/ols4/ontologies/stato"                            
#> [18,] "[,, \"no database\", null ]"                                            
#> [19,] "null"                                                                   
#> [20,] "Unknown"                                                                
#> [21,] "null"                                                                   
#> [22,] "[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]"                
#> [23,] "[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]"                
#> [24,] "[MS, MS:1002896, compound identification confidence level, ]"           

mtd
#>       [,1]                                        
#>  [1,] "mzTab-version"                             
#>  [2,] "mzTab-ID"                                  
#>  [3,] "mzTab-profile"                             
#>  [4,] "software[1]"                               
#>  [5,] "quantification_method"                     
#>  [6,] "cv[1]-label"                               
#>  [7,] "cv[1]-full_name"                           
#>  [8,] "cv[1]-version"                             
#>  [9,] "cv[1]-uri"                                 
#> [10,] "cv[2]-label"                               
#> [11,] "cv[2]-full_name"                           
#> [12,] "cv[2]-version"                             
#> [13,] "cv[2]-uri"                                 
#> [14,] "cv[3]-label"                               
#> [15,] "cv[3]-full_name"                           
#> [16,] "cv[3]-version"                             
#> [17,] "cv[3]-uri"                                 
#> [18,] "database[1]"                               
#> [19,] "database[1]-prefix"                        
#> [20,] "database[1]-version"                       
#> [21,] "database[1]-uri"                           
#> [22,] "small_molecule-quantification_unit"        
#> [23,] "small_molecule_feature-quantification_unit"
#> [24,] "small_molecule-identification_reliability" 
#>       [,2]                                                                     
#>  [1,] "2.1.0-M"                                                                
#>  [2,] "001"                                                                    
#>  [3,] "M"                                                                      
#>  [4,] "[MS, MS:1001582, xmcs, 4.0.0]"                                          
#>  [5,] "[MS, MS:1001834, LC-MS label-free quantitation analysis, ]"             
#>  [6,] "MS"                                                                     
#>  [7,] "PSI-MS controlled vocabulary"                                           
#>  [8,] "4.1.138"                                                                
#>  [9,] "https://www.ebi.ac.uk/ols4/ontologies/ms"                               
#> [10,] "PRIDE"                                                                  
#> [11,] "PRIDE PRoteomics IDEntifications (PRIDE) database controlled vocabulary"
#> [12,] "16:10:2023 11:38"                                                       
#> [13,] "https://www.ebi.ac.uk/ols/ontologies/pride"                             
#> [14,] "STATO"                                                                  
#> [15,] "General purpose STATistics Ontology"                                    
#> [16,] "2026-04-20"                                                             
#> [17,] "https://www.ebi.ac.uk/ols4/ontologies/stato"                            
#> [18,] "[,, \"no database\", null ]"                                            
#> [19,] "null"                                                                   
#> [20,] "Unknown"                                                                
#> [21,] "null"                                                                   
#> [22,] "[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]"                
#> [23,] "[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]"                
#> [24,] "[MS, MS:1002896, compound identification confidence level, ]"