Man pages for taylo5jm/interactions
Classification of gene expression profile sets generated from combination stimuli
| allDrugCombinations | Get all drug combinations present in a MySQL database |
| allModes | Generate character vector of all possible interaction mode... |
| asCountsMatrix | Strip counts data.frame of any extra variables |
| classifyByThOutcomeVector | Classify a gene into an interaction mode given an outcome... |
| codeEdgeROutcomeVectors | Code pairwise comparison outcome vectors with edgeR... |
| codeLimmaOutcomeVectors | code pairwise comparison outcome vectors with limma |
| codeOVElement | Code elements of pairwise outcome vectors with confidence... |
| colorBarplot | Color bars in geom_bar plot given an interaction class and... |
| comboExists | return boolean indicating if drug combination was found in... |
| comboIndices | return signal combination indices in treatment/concentration... |
| designColnames | check column names of design matrix |
| designMatrixAndContrasts | make design matrix and contrasts based on whether... |
| dge2voom_q | calculate normalization factors with edgeR and voom with... |
| edgeRModeClassifier | Interaction mode classification with edgeR likelihood ratio... |
| enumerateThOutcomeVectors | Enumerate theoretical pairwise comparison outcome vectors... |
| estimateAllGLMDisp | Fit generalized linear model and make pairwise comparisons... |
| filterMetadata | Filter data.frame of libraries retrieved by attributes such... |
| getCondition | Retrieve libraries treated with a particular condition and... |
| getExpectedCounts | Get matrix of expected counts from rnaseq_assay_id |
| getGeneMetadata | Get data.frame with gene metadata |
| getGeneVector | Get binary factor vector for genes |
| getGOTable | Generate gene ontology table and data with topGO from... |
| getGOTermsForAllModes | get GO tables for all ontologies, given an interaction table... |
| getGOTermsForModes | get topGO tables and significant genes for a particular... |
| getIntClass | Get character string classification for interaction class |
| getInteraction | Get libraries for a specified signal interaction |
| getPCAScores | Principal Component Analysis scores using log-fold changes as... |
| getVehicles | Get vehicles for libraries of interest |
| glmFitAndLRT | generalized linear model and likelihood ratio tests with... |
| initInteraction | initalize an Interaction object from a list generated with... |
| Interaction-class | Interaction class to hold results from mode classification... |
| interactionDistTable | Generate table with outcome vectors, interaction classes &... |
| interactionGeneTable | Generate table with genes classified into a mathematically... |
| interactionModeClassifier | Interaction mode classification with limma and edgeR |
| interactions-package | interactions |
| isAnomaly | Determine if an outcome vector is enumerated theoretically |
| isMode | Check to see if an outcome vector is associated with a... |
| isNi | check outcome vector to see if it is consistent with 1/5... |
| isValidCombination | Check to see if a drug combination exists in eld_v4 |
| limmaModeClassifier | Interaction mode classification with matrix of counts and... |
| massageCounts | apply expected counts filter to DGEList object Aaron Mackey |
| modeClassification | Interaction mode classification with matrix of outcome... |
| multiplot | Plot an arbitrary number of graphics on one page Credits to... |
| niCheck | Check to see if an outcome vector is consistent with a... |
| outcomeVectorsByMode | Generate a list where each element is a matrix/vector of... |
| ovTable | generate frequency distribution table for outcome vectors |
| partitionData | partition feature vectors (pca_scores) and interaction mode... |
| pcaScatterMatrix | Make scatter matrix from PCA scores |
| poolInteractionGenes | Generate interaction table with genes classified into... |
| qplotOutcomeVectorDist | Make barplot of outcome vector distribution with... |
| rankTuples | Compute row ranks and average ties (should be deprecated) |
| reportModeClassStats | Print statistics about the interaction mode distribution and... |
| reportnAnomaly | Report number of genes classified into an anomalous mode... |
| reportnInteractions | Report number of genes classified into a non-null or... |
| reportnNI | Report number of null interaction vectors coded |
| saveTopGoRes | save topGO table as .csv and topGO DAG as .png |
| sharedGenesTable | Create data.frame for genes that were classified into modes... |
| sitt-package | Signal Interaction Tools for Transcriptomics ~~ sitt ~~ |
| stringCoerce | Coerce a numeric vector to a string the wrong way |
| trainKNN | train k-nearest neighbours model with pca scores as feature... |
| treatmentConcTable | Generate a table of all treatment/concentration conditions... |
| tuneClassifier | Evaluate model performance by initializing many analysis... |
| uniqueBatches | Get vector of unique batches retrieved from a particular... |
