Man pages for thomazbastiaanssen/anansi
Annotation-Based Analysis of Specific Interactions
| anansi | Calculate an association network |
| anansi_compute_clr | compute CLR using Aitchison's method |
| anansiCor | Compute r-statistics for each featureY-featureX pair in the... |
| anansiCorPvalue | Compute r-statistics for each featureY-featureX pair in the... |
| anansiCorTestByGroup | Run correlations for all interacting metabolites and... |
| anansi_dic | Dictionary to link KEGG compounds to KEGG orthologues |
| anansiDiffCor | Run differential correlation analysis for all interacting... |
| anansiInput-class | An S4 class to contain all 'anansi' input so that they can... |
| anansiOutput-class | An S4 class to contain all 'anansi' output so that they can... |
| anansiTale-class | An S4 class to contain all 'anansi' stats results so that... |
| anansiTranslate | Translate tableY and tableX columns column to human readable... |
| anansiWeb-class | An S4 class to contain all metabolomics and functional input... |
| anansiYarn-class | An S4 class to contain all 'anansi' input and output so that... |
| argonansiWeb-class | An S4 class to contain all metabolomics and functional input... |
| argonaut_parse_diff | Parse argonansi output |
| argonaut_parse_full | Parse argonansi output |
| argonaut_parse_tot | Parse argonansi output |
| argonaut_rep_to_strat | Expand a matrix of dictionary dimensions to stratified... |
| assessWebCall | Helper function to assess the input feature tables |
| clr_imputed | Resample random values, perform CLR over each iteration and... |
| clr_lite | Impute zeroes and perform a centered log-ratio (CLR)... |
| collate_model_output_argonaut | Run differential correlation analysis for all interacting... |
| cpd_translation | Lookup table to convert KEGG compound IDs to their... |
| FMT_KOs | Snippet of the untransformed inferred functional data from... |
| FMT_metab | Snippet of the CLR-transformed hippocampal metabolomics data... |
| FMT_metadata | Snippet of the metadata from the FMT Aging study. |
| gather_plot | Take anansi output and wrangle it to a list of plottable... |
| getAnansi | anansi wrapper for the MultiAssayExperiment class |
| getAnansiResults | Extract information from an anansiTale object and parse it... |
| get_strat_X | Collapse tableX for Argonaut data |
| glm_argonaut_calc_diff_cor | Run differential correlation analysis for all interacting... |
| impute_zeroes | Replace zeroes with non-zero values in order to perform a... |
| KO_member_dic | Dictionary to link KEGG orthologues based on their pathway... |
| KO_translation | Lookup table to convert KEGG orthologue (KO) IDs to their... |
| makeAdjacencyMatrix | Starting point to wrangle anansi dictionary list into binary... |
| makeAdjacencyMatrixFromGroupMemberList | Wrangle anansi dictionary list into binary adjacency matrix |
| makeAdjacencyMatrixFromList | Wrangle anansi dictionary list into binary adjacency matrix |
| mock_dictionary | Helper function to make a mock dictionary |
| plot-anansiYarn-ANY-method | Plotting method for 'anansiYarn' object. |
| print-anansiYarn-method | Print method for 'anansiYarn' object. |
| prune_dictionary_for_exclusivity | Kick out particularly large groups before wrangling the... |
| show-anansiYarn-method | Show method for 'anansiYarn' object. |
| softmax | Undo CLR transformation with softmax |
| spinToLong | Take anansi output and wrangle it all to a long data.frame... |
| spinToPlots | Take anansi output and wrangle it to a list of plottable... |
| spinToWide | Take anansi output and wrangle it all to a wide data.frame... |
| summary-anansiYarn-method | Summary method for 'anansiYarn' object. |
| weaveWebFromStratifiedTables | Create an argonansiWeb object from two 'omics tables and a... |
| weaveWebFromTables | Create an anansiWeb object from two 'omics tables and a... |
