Table 1.
Comparison of the CAMERA.annotate and ACorF tool functionalities.
| - | CAMERA.annotate (W4M version) | “Analytic Correlation Filtration” (ACorF) Tool |
|---|---|---|
| Interface | Galaxy (W4M) | Galaxy (W4M) |
| Language | R | Perl |
| Version | Galaxy version 2.1.3 | - |
| Input files | .Rdata output from XCMS Galaxy pre-processing | DataMatrix, variableMetadata and similarity matrix |
| Parameters | - | - |
| Mandatory | - | Correlation rate Representative selection method |
| Optional | Correlation rate RT window determination variables | Mass difference list Retention time tolerance delta |
| Correlation information | Calculation of correlation is included in the tool | A correlation table has to be obtained before using the tool |
| Correlation type | Pearson correlation | Any type of correlation are possible |
| Possibility to set a Correlation threshold | Yes—only for the second step of grouping | Yes |
| Retention time (RT) window | Calculated for each peak | Defined by a threshold |
| Parameter settings | Two different parameters ([sigma] and [perfwhm]) are available | The user can set the RT tolerance delta value |
| Comparison to a mass defect list | Conditioned by obtained group but not used for grouping | When used, directly impact the group determination |
| Isotope identification | Yes—performed in a previous step | Yes—if the isotope mass difference is included in the list |
| Existing default list | Yes | Yes |
| Possibility to upload a personal list | Yes | Yes |
| Possibility of setting a mass difference tolerance value | No | Yes |
| Possibility of selecting a representative ion for each group | No | Yes |
| Output files | variableMetadata with additional columns | variableMetadata with additional columns and a .sif file for network visualisation |
| Optional output files | EIC for main pc-group visualisation pdf file | - |