Man pages for MetamapsDB
Network Analysis of Metabolic Pathways and Gene Based Assemblies in Metagenomics
| addContigProperty | addContigProperty |
| addKOProperty | addKOProperty |
| adjacentPairs | Given a igraph object, adjacentPairs finds adjacent pairs of... |
| allTrios | Find all trios surrounding the KO of interest |
| annotateContigs.taxonomy | Adds taxonomic annotations of the contigs |
| blatting | blatting |
| buildE | buildE sorts the tree into a data.frame |
| buildTree | Taxonomic tree of the taxons |
| categorize | categorize |
| connect | Connecting to NEO4J Graph Database. |
| contigInfo | contigInfo |
| contigsSurvive.repeats.readNum | contigsSurvive.repeats.readNum |
| contigsSurvive.repeats.rpk | contigsSurvive.repeats.rpk |
| contractMetab | contractMetab shrinks a metabolic network's KOs into... |
| cpdname | Finds the details of the CPD when given its ID |
| dbquery | Function for querying metamaps DB |
| dollarpipe | with Pipe operator |
| doublepipe | Double Pipe operator |
| dynamicThreshold | dynamicThreshold tries to identify the lower bound converage... |
| dynPlots | dynPlot Diagnostic plots |
| extractFromPath | extractFromPath |
| findHomology | searches for KO's homology assignments |
| findK | findK to find the optimum number of Ks |
| findNextKO | FindNextKO |
| findPerl | findPerl finds the path to the executable |
| findPython | findPython finds the path to the executable |
| findSeeds | To find all seed compounds in the metabolic graph |
| findTrios | findTrios searches valid three-KO reactions resticting by the... |
| findtype | findType finds KOs/compounds ID in metabolic graph |
| findV | findV finds the vertixID in the graph given its name |
| grep.cDNA | grep.cDNA |
| grepgraph | Returns the metabolic graph given vector of KOs |
| grepgraph_cpd | Generates metabolic network as IGRAPH object from input... |
| grepgraph.cpd | Returns the metabolic graph given vector of KOs |
| grepReads | grepReads greps for cDNA or gDNA reads cause they are both... |
| ig2ggplot | Convert igraph to ggplot2 object |
| igraph2gexf | Converts igraph obj two gexf Function for converting igraph 2... |
| index | Indexes the database for faster retrieval |
| ko2path | ko2path Finds all pathways related to the KO Finds all... |
| koname | Gives KO details when supplied with KO id |
| ksCal | ksCal generates KS statistics for aKO given the base... |
| lca | Finds the lowest common ancestor |
| listquery | Function for querying metamaps DB |
| lookupTable | generates 'lookupTable' for filtering raw data post gene... |
| make.data.frame | Convert columns with nested list structures into plain... |
| map | map takes cDNA reads (fastQ format) and maps them onto... |
| mapContig | finds the location of the MDR on the contig |
| mappingInfo | mappingInfo sequence analysis of contigs (for SIMULATION... |
| mapReads2MDR | overlaps |
| mdrRanges | Returns contig ranges for those captured within the MDR |
| nitrogenMetab | nitrogenMetab |
| path2kingdom | List all intermediaries between taxa and the superkingdom it... |
| path2ko | Finds all KOs in a given pathway Finds all KOs belonging to a... |
| pathways | List Pathways Lists all metabolic pathways |
| pipe | Pipe operator |
| plotClassification | Plot clustering |
| prettifyGraph | returns metabolic graph with all the ornaments set Adds... |
| readStatusReader | readStatusReader stores read assignment details from the... |
| rolling | rolling A dynamic threshold for the killing redundant contigs |
| scg | singleCopyGenes' |
| simpleThres | simpleThres |
| simulated | finds all simulated genera for that particular KO |
| surrNODES | surrNODES finds nodes which are surrounding the given node |
| taxname | Lists the taxonomic id's details |
| taxnam.sql | taxname.sql |
| top500kos | Top500kos |
