A map alignment algorithm based on pose clustering.
Pose clustering analyzes pair distances to find the most probable transformation of retention times. The algorithm choses the x most intensity peaks/features per map. This is modeled via the parameter 'max_num_peaks_considered', which in turn influences the runtime and stability of the results. Bigger values prolong computation, smaller values might lead to no or unstable trafos. Set to -1 to use all features (might take very long for large maps).
| Name | Type | Default | Restrictions | Description |
|---|
| max_num_peaks_considered |
int | 1000 |
min: -1 | The maximal number of peaks/features to be considered per map. To use all, set to '-1'. |
| superimposer:mz_pair_max_distance |
float | 0.5 |
min: 0 | Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing. |
| superimposer:rt_pair_distance_fraction |
float | 0.1 |
min: 0 max: 1 | Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min). |
| superimposer:num_used_points |
int | 2000 |
min: -1 | Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1. |
| superimposer:scaling_bucket_size |
float | 0.005 |
min: 0 | The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs. |
| superimposer:shift_bucket_size |
float | 3 |
min: 0 | The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans. |
| superimposer:max_shift |
float | 1000 |
min: 0 | Maximal shift which is considered during histogramming. This applies for both directions. |
| superimposer:max_scaling |
float | 2 |
min: 1 | Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this. |
| superimposer:dump_buckets |
string | |
| [DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically. |
| superimposer:dump_pairs |
string | |
| [DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically. |
| pairfinder:second_nearest_gap |
float | 2 |
min: 1 | The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself. |
| pairfinder:use_identifications |
string | false |
true, false | Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account). |
| pairfinder:ignore_charge |
string | false |
true, false | Compare features normally even if their charge states are different |
| pairfinder:distance_RT:max_difference |
float | 100 |
min: 0 | Maximum allowed difference in RT in seconds |
| pairfinder:distance_RT:exponent |
float | 1 |
min: 0 | Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
| pairfinder:distance_RT:weight |
float | 1 |
min: 0 | RT distances are weighted by this factor |
| pairfinder:distance_MZ:max_difference |
float | 0.3 |
min: 0 | Maximum allowed difference in m/z (unit defined by 'unit') |
| pairfinder:distance_MZ:unit |
string | Da |
Da, ppm | Unit of the 'max_difference' parameter |
| pairfinder:distance_MZ:exponent |
float | 2 |
min: 0 | Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
| pairfinder:distance_MZ:weight |
float | 1 |
min: 0 | m/z distances are weighted by this factor |
| pairfinder:distance_intensity:exponent |
float | 1 |
min: 0 | Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
| pairfinder:distance_intensity:weight |
float | 0 |
min: 0 | Distances based on relative intensity are weighted by this factor |
