Man pages for acorg/acutilsLite
A package for working with CPE databases
| acdb.applyFunction | Apply a function over an acdb |
| acdb.as.list | Convert database entries to lists |
| acdb.extract | Match and extract a single entry from attributes |
| acdb.find | Match attributes |
| acdb.getIDs | Subset database based on IDs |
| acdb.idToAttr | Get named attribute from acdb |
| acdb.matchNames | Find name matches in an antigen or serum database |
| acdb.matchNamesIndices | Function to find db entries with names matching passed strain... |
| acdb.matchSubstitutions | Find db entries with same subsititutions as subs |
| acdb.matchSubstitutionsIndices | Find db entries with same subsititutions as subs |
| acdb.nameIDs | Get long names from acdb |
| acdb.search | Match and extract attributes |
| acdb.slice | Subsetting for databases |
| ac.exp | Experiment |
| acids.applyFunction | Apply a function over an acdb subset, found by id |
| ac.inGroups | Check if ag/sr is in groups |
| ag | Antigen |
| ag.attribute | Get gene attribute |
| ag.children | Get children |
| ag.clade | Get antigen clade You can choose whether clade is searched... |
| ag.clade.self | Get antigen clade |
| ag.cluster | Get antigen cluster |
| agdb | Antigen database |
| agdb.ag | Produce an antigen entry for the database |
| agdb.alterations | Constructs an antigen alterations entry |
| agdb.append | Append an antigen to an agdb |
| agdb.checkAG | Check antigen entry formatting |
| agdb.checkagdb | Checks Antigen Database formatting |
| agdb.checkalterations | Check an antigen alterations entry |
| agdb.checkgenes | Check an antigen genes entry |
| agdb.checkid | Check an id |
| agdb.checkisolation | Check an antigen isolation entry |
| agdb.checkpassage | Check a passage entry |
| agdb.clusters | Get ag clusters from acdb |
| agdb.experiments | Get experiments that antigens are in |
| agdb.genes | Constructs an antigen gene entry |
| agdb.getIDs | Subset antigen database based on IDs |
| agdb.hasSubstitutions | Are there subsitutions in the inheritance of HA? |
| agdb.homologousSera | Get homologous sera |
| agdb.id | Generate an id |
| agdb.isolation | Constructs an antigen isolation entry |
| agdb.merge | Merge antigens in agdb |
| agdb.new | Create antigen database |
| agdb.passage | Constructs an antigen passage entry |
| agdb.sequencesFromMap | Get sequences from agdb |
| agdb.substitutions | Get substitutions from agdb |
| ag.descendents | Get all descendants |
| ag.descendentsTree | Get all descendants |
| ag.duplicate | Duplicate an antigen entry |
| ag.experiments | Get experiments that an antigen is in |
| agid.cluster | Get antigen cluster |
| ag.inheritance | Get inheritance list for a gene. |
| ag.long | Get long name for an antigen |
| ag.parent | Get parent |
| ag.passageChildren | Get passage children |
| ag.passageChildrenFlat | Get all passage descendants |
| ag.passageChildrenTree | Get all passage descendants |
| ag.passageInheritance | Get passage inheritance |
| ag.passageParent | Get passage root |
| ag.passageSiblings | Get all antigens which differ only by passage |
| ag.root | Get antigen root |
| ag.sequence.allVariants | Calculate gene sequence |
| ag.sequence.calculate | Calculate sequence for a gene from an inheritance (by finding... |
| ag.sequence.pluck | Get sequence for a gene from a record |
| ag.short | Construct short name for an antigen |
| ag.standardlong | Get standardised long name for an antigen |
| ag.substitutions | Get gene substituions for antigen |
| as.list.acdatabase.ag | Convert database entry to list |
| cash-.acdatabase.entry | Subsetting for acdb entries |
| check_condition | Check if a condition is fulfilled |
| collate | List to vector |
| combineTiters | Combine titers |
| expdb | Experiment database |
| expdb.ags | Get antigens in expdb |
| expdb.merge | Merge from expdb |
| expdb.sr | Get sera in expdb |
| expdb.toLongTibble | Parse an expdb to tibble |
| exper.merge | Merge from exp |
| exper.toLongTibble | Parse an experiment to tibble |
| grapes-cash-grapes | Subsetting for databases |
| grapes-cash-grapes-set | Assignment for databases |
| h3_clade_grouping_heirarchy | order for matching |
| h3_clade_order | order for plotting |
| is.substitution | Check a substitutions entry |
| logtiter.toPlot | this converts logtiters with less thans to logtiters where <3... |
| longtiters.addRecords | Add ag, sr, exp records from IDs to tibble |
| longtiters.colbase | Colbase titers |
| longtiters.plotdata | Add tibble plotting columns |
| mergeTiters | Merge titers |
| outbox.agdb.database | Mark which properties should be unboxed |
| outbox.srdb | Mark which properties should be unboxed |
| place_abvs | All known two-letter place name abbreviations |
| print.acdatabase.entry | Printing an acdb entry |
| read.agdb | Read database |
| read.srdb | Read database |
| result.titerTable | Get titer table from result entry |
| sequences_plot | Make sequence comparison plot |
| sr | Serum |
| sr.attribute | Get serum attribute |
| sr.children | Get children |
| sr.cluster | Get serum cluster |
| srdb | Serum database |
| srdb.append | Append a serum to an srdb |
| srdb.clusters | Get sera clusters |
| srdb.getIDs | Subset serum database based on IDs |
| srdb.homologousAntigens | Get homologous sera |
| srdb.id | Generate an id |
| srdb.matchAnimalIDs | Find sera matching an animal id |
| srdb.matchAnimalIDsIndices | Find sera matching an animal id |
| srdb.merge | Merge sera in serum database |
| srdb.new | Create serum database |
| srdb.sr | Produce a serum entry for the database |
| sr.experiments | Get experiments that a serum is in |
| srid.cluster | Get serum cluster |
| sr.inheritance | Get inheritance list for a serum. |
| sr.parent | Get parent |
| standardizeStrainName | Function for standardising names locally |
| standardizeStrainNames | Standardize strain names |
| sub-.acdatabase.entry | Subsetting for acdb entries |
| subs.split | Split substitutions to get from, at, to |
| summarise_plotdata_by_ag_cluster | Summarise by antigen cluster |
| summarise_plotdata_by_sr_cluster | Summarise by serum cluster |
| tibble.factorize | convert column(s) into factor for plotting |
| titers.getThresholds | find out what thresholded titer values are present |
| titers.toNumeric | remove less thans or greater thans |
| titer.toLog | titer to logtiter |
| titer.toPrint | ? |
| write.agdb | Write database to file |
| write.srdb | Write database to file |
