ectra < csm_spectra
MS spectral Object. Contains X, X scale and various metadata.
ms_features object is accessed using the identifier specified in the
x_scale and x_scale_name. It's up to you make sure you do this correctly.
Extends csm_spectra; see csm_spectra for more information.
csm_nmr_spectra.getSubSpectra( conditions ) will return a spectra based on the fields in sample_metadata.
conditions is the format {{ field, condition }}, and multiple conditions can be specified
ie:
conditions = {{ 'HistoScore', 'HS2' } ,{ 'RatNumber', '34' }}
spectra = csm_ms_spectra( X, x_scale, x_scale_name );
spectra = csm_ms_spectra( X, x_scale, x_scale_name, 'ms_type', ms_type, 'name', name, 'is_continous', is_continuous, 'sample_ids', sample_ids, 'sample_metadata', sample_metadata, 'ms_features', ms_features );
| Variable | Type | Default Value | Description |
|---|---|---|---|
| *X | m*n | None | spectral matrix. |
| *x_scale | 1*n | None | X Scale, the X scale used in this dataset, ie retentionTime_mz. |
| *x_scale_name | str | None | The name of X scale, ie 'retentionTime_mz'. |
| ms_type | str | None | The type of MS, 'LC-MS', 'HPLC-MS', 'GC-MS', 'UPLC-MS', 'Direct Injection','HPLC-MS'. |
| name | str | None | Name of the data structure. |
| is_continuous | bool | true | Whether the x scale is continuous |
| sample_ids | cell | {} | Sample IDs, Use the numeric index to match to the row |
| csm_sample_metadata | csm_sample_metadata | [] | Sample Metadata |
| ms_features | map | empty | Container of features |
| Variable | Type | Description |
|---|---|---|
| csm_ms_spectra | csm_ms_spectra | CSM MS spectra object. |
| csm_ms_spectra.X | m*n | spectral Matrix. |
| csm_ms_spectra.x_scale | 1*n | PPM Scale. |
| csm_ms_spectra.name | str | Name of the object. |
| csm_ms_spectra.sample_ids | cell | Sample IDs, using a numeric index. |
| csm_ms_spectra.sample_metadata | csm_import_sample_metadata | Metadata from import. |
| csm_ms_spectra.auditInfo | csm_audit_info | Audit Info object. |
| csm_ms_spectra.ms_features | csm_ms_features | Container of features |
Copyright Imperial College London 2019