Man pages for krisrs1128/phyloseqExtend
Extend Phyloseq to Rich Data Types
| add_dim_names | Add default row and column names for a spectra object |
| add_plot_layers | Helper to add layers to ggplot plot |
| align_spectra | Wrapper for removeBaseline and alignSpectra in MALDIquant |
| filter_nonzero | Vectorized filter function in the spirit of k over a |
| filter_variance | Vectorized variance filtering |
| get_annotation | Helper to get annotation list from a physeq object |
| get_authors | Get authorship data associated with a UniProt XML |
| get_citation | Get citation data associated with a UniProt XML |
| get_comment | Get comment data associated with a UniProt XML |
| get_db_ref | Get database data associated with a UniProt XML |
| get_gene | Get gene data associated with a UniProt XML |
| get_organism | Get organism data associated with a UniProt XML |
| get_peaks_list | Wrapper for MALDIquant detectPeaks |
| get_ppm | Get ppm values associated with a spectra matrix |
| get_protein | Get protein data associated with a UniProt XML |
| get_sequence | Get sequence data associated with a UniProt XML |
| get_source | Get source data associated with a UniProt XML |
| get_spectra_at_peaks | Extract Spectra at Peak Positions |
| get_spectra_at_peaks_zeros | Extract Spectra at Peak Positions, with zeros for non-peaks |
| get_uniprot_info | Extract information from UniProt Accession ID |
| interpolate_duplicates | Interpolate Duplicated Values |
| merge_ctable_opts | Merge default contingency table processing options |
| merge_spectra_opts | Merge default spectra processing options |
| phyloseqExtend | Assemble several data objects into a phyloseqExtend object. |
| phyloseqExtend-class | The high-level extended phyloseq object, including new slot... |
| plot_raw_spectra | Plot Raw Spectra Intensities Across All Indices |
| plot_spectra | Plot Spectra Intensities |
| plot_spectra_peaks | Plot only the Peaks in a spectra matrix |
| process_ctable | Wrapper for contingency table processing |
| process_spectra | Wrapper for processing spectra matrices |
| prune_samples-character-spectra-method | Define a prune_samples methods for spectra class |
| remove_baseline | Wrapper for removeBaseline and alignSpectra in MALDIquant |
| remove_outlier_spectra | Remove Outliers |
| row_var | Fast row variance |
| rpkg_from_rpkm | Compute RPKGs from RPKMs |
| show-phyloseqExtend-method | Print a phyloseqExtend object |
| spectra | Build or access an object of class spectra |
| spectra-class | The S4 class for storing metabolomic information |
| spectraOrNull-class | spectra S4 class with placeholder |
| subsample_spectra_cols | Subsample spectra and filter spectra to range based on column... |
| subset_samples_spectra | Subset the samples of an object of class spectra |
