Man pages for VEuPathDB/veupathUtils
General Helper Functions for VEuPathDB Projects
| as.numeric-BinList-method | Convert bins in a BinList with character start and end values... |
| as.numeric-Bin-method | Convert a Bin with character start and end values to numeric |
| Bin-class | Bin |
| Collection-class | Data Collection |
| Collection-methods | Create a Collection |
| Collections-class | Data Collections |
| Collections-methods | Create Collections |
| CollectionWithMetadata-class | Collection With Metadata |
| Comparator-class | Comparator |
| ComputeResult-class | Compute Result |
| correlation | Correlation |
| CorrelationResult-class | Corrleation Result |
| CountDataCollection-class | Count Data |
| cut_interval | Discretise numeric data into equal ranges |
| cut_number | Discretise numeric data into equal size groups |
| cut_width | Discretise numeric data into equal ranges |
| data_frame | Fast data.frame |
| differentialExpression | Differential expression |
| findAllColNames | All EDA Variable Column Names |
| findCollectionVariableMetadata | EDA Variable Metadata matching a Collection |
| findColNamesByPredicate | Find EDA column names |
| findColNamesFromPlotRef | EDA Variable Column Names matching a PlotReference |
| findDataShapesFromPlotRef | EDA Variable Data Shapes matching a PlotReference |
| findDataTypesFromPlotRef | EDA Variable Data Types matching a PlotReference |
| findIndexFromPlotRef | EDA Variable index matching a PlotReference |
| findNumericCols | Find numeric columns |
| findStudyDependentVocabularyVariableMetadata | EDA Variable Metadata with a Study-dependent Vocabulary |
| findVariableMetadataFromPlotRef | EDA Variable Metadata matching a PlotReference |
| findVariablesNeedingWeightingVariableMetadata | EDA Variable Metadata which needs weighting |
| findVariableSpecFromPlotRef | EDA Variable Spec matching a PlotReference |
| findWeightingVariablesMetadata | EDA VariableMetadataList matching any weightingVariableSpec |
| getAggStr | Make Aggregation Formulas |
| getCollectionData | Get data.table of values from Collection |
| getCollectionNames | Get Names of Collections |
| getCollectionVariableNames | Get Collection Variable Names |
| getColName | EDA Variable Column Name of a VariableSpec |
| getDataTable | Convert StatisicList to data.table |
| getDiscretizedBins | Find Bin Ranges for a Continuous Variable |
| getDTWithImputedZeroes | Impute Zeroes (on tall data) |
| getGroupLabels | Get labels from a group in a Comparator |
| getIdColumns | Get all ID columns |
| getMetadataVariableNames | Get Variable Names of Metadata |
| getMetadataVariableSummary | Get Summary of Metadata Variables |
| getSampleMetadata | Get data.table of sample metadata from CollectionWithMetadata |
| getSampleMetadataIdColumns | Get Sample Metadata Id Column Names |
| getStudyIdColumnName | StuydIdColName as String |
| getVariableSpec | get a VariableSpec |
| getVariableSpecColumnName | VarSpecColName as String |
| is.error | Try-error Test |
| isOneToManyWithAncestor | Is One to Many With Ancestor |
| is.POSIXct | POSIXct Test |
| logWithTime | Diagnositc Messages with Time of Occurance |
| matchArg | Character and Logical Argument Verification |
| Megastudy-class | Megastudy |
| megastudyDataReal | Some Real Life Popbio Megastudy Test Data |
| merge | Merge Variable*List objects |
| name | Manage Collection Names |
| naToZero | Replace numeric NAs with 0 |
| nonZeroRound | Non-Zero Rounding |
| pca | PCA |
| predicateFactory | Predicate Factory |
| predicateFactory-character-numeric-method | Predicate Factory |
| pruneFeatures | Prune features by predicate |
| Range-class | Data Range |
| removeIncompleteRecords | Drop Records with incomplete SampleMetadata |
| SampleMetadata-class | Sample Metadata |
| selfCorrelation | Self Correlation |
| setAttrFromList | Set object attributes from a list |
| setNaToZero | Replace numeric NAs with 0 - update by reference |
| setroworder | Set Row Order |
| shiftToNonNeg | Shift Values to be non-negative |
| Statistic-class | Statistic |
| stripEntityIdFromColumnHeader | Strip Entity ID from Column Header |
| strSplit | Efficient Vectorized String Split |
| StudySpecificVocabulariesByVariable-class | Study Specific Vocabularies By Variable |
| toJSON | R object as JSON string |
| toStringOrNull | Replace Empty String with NULL |
| trim | Trim White Space |
| validateNumericCols | Validate numeric columns |
| VariableSpec-class | Variable Specification |
| veupathUtils-package | veupathUtils: General Helper Functions for VEuPathDB Projects |
| whichValuesInBin | Find values that fall within a Bin |
| whichValuesInBinList | Find values in a vector that fall within any bins in a... |
| writeData | Write Compute Result Data |
| writeMeta | Write Computed Variable Metadata |
| writeStatistics | Write Computed Variable Statistics |
