Man pages for RGLab/ImmuneSignatures2
Pre-Processing for HIPC ImmuneSignatures2 Analysis
| addAnalysisVariables | Add demographic variables needed for analysis |
| addArmAccession | Add Arm Accession to meta-data |
| addCoalescedFeatureSetName | Create new featureSetName field that coalesces similar... |
| addDemographicFields | Add fields from demographic data to meta-data |
| addFeatureAnnotationSetName | Add name of feature annotation set name used to generate gene... |
| addFeatureAnnotationSetVendor | Add name of feature annotation set vendor used to generate... |
| addGeBatchName | Add geBatchName for use in cross-study normalization |
| addGSMAccessions | Add name of feature annotation set vendor used to generate... |
| addIrpBatchName | Add irpBatchName for use in responseCall generation |
| addMatrixRelatedFields | Add matrix, featureset, and cell_type fields to pData objects |
| addResponseData | Add selected immune response data to final expressionSets |
| addSDY1325metadata | Add fields from SDY1325 custom meta-data to shared meta-data |
| addStudy | Add Study to meta-data |
| addTimePostLastVax | To accomodate studies with booster shots, add a timepoint... |
| addVaccineFields | Add fields from vaccine data to meta-data |
| ageGroups | Age groups for determining age cohorts |
| all_genesets | Gene sets used in the pre-vaccination manuscript |
| batchCorrect | Adjust expression data using correction coefficients based on... |
| batchCorrect.importedModel | Adjust baseline expression data to account for... |
| checkFinalTestResults | Ensure eset is as expected |
| correctHrs | Convert 'Hours'-based study times to 'Days'-based |
| createUniqueIdColumn | Generate a unique id column |
| crossStudyNormalize | Cross-Study normalize an expressionSet object based on a... |
| customProcessing | Custom pre-processing for particularly ornery studies |
| expectedGeMetaDataColumns | Expected Gene Expression Meta-Data columns |
| filterEsetByAge | Filter expressionSet by age cutoffs |
| filterImmdataByAge | Filter immdata list elements by age filter |
| filterOutNoVaccineSamples | Filter out cohorts with no vaccine data from custom mapping |
| generateELISAResponse | Generate immune response call for age specific ELISA cohort |
| generateNAbHAIresponse | Generate immune response calls for HAI or NAb using pipeline... |
| generateResponseCall | Generate immune response calls for HAI, NAb or ELISA |
| getImmuneResponseData | Function generates a base dataset from ImmuneSpace |
| getLmFitValues | Get linear model fit values for each gene |
| getModelFormula | Get linear model formula |
| getTable | Get a backend table not easily accessible through... |
| imputeAge | Impute age for those with missing age values or ranges given... |
| imputeYchrom.useAllTimepoints | Impute presence of y chromosome based on expression of Y... |
| performTiterAnalysis | Flexible function that wraps around 'titer::Calculate'... |
| preProcessImmData | Pre-processing for 'titer::Calculate' functions |
| qualityControl.createSubjectsByStudyTable | Generate table of studies with count of participants from... |
| qualityControl.failedYchromQC | Generate ychrom box plots after QC |
| qualityControl.genderByMatrix | Generate gender box plots (prior to QC) |
| qualityControl.samplePlot | Generate sample MDS plots for QC |
| qualityControl.yChromPresentByMatrix | Generate box plots showing ychrom imputed after QC |
| relevelEsets | Get linear model fit values for each gene |
| removeAllNArows | Remove incomplete rows |
| removeSDY212MissingSample | SDY212 has a biosample that does not have matching meta-data... |
| removeTimepointFromEset | Remove samples from certain timepoints from desired studies |
| runAllAnalyses | run both maxRBA and MFC calculations using the 'titer'... |
| sdy1325_metadata | SDY1325 meta-data Derived from study-associated paper's... |
| sdy1370_elisa | SDY1370 ELISA data |
| selectResponsesToUse | Generate a single response call data.table from multiple... |
| subsetToOnlyNeededColumns | Subset to just columns needed for cross-study normalization... |
| summarizeByGeneSymbol | Summarize probe-level gene expression data by gene symbol... |
| testAllGEMatrixPreNorm | Test gene expression matrix of all samples prior to... |
| testAllGEMetaDataPreNorm | Test gene expression meta-data of all samples prior to... |
| testExtractedGEData | Test gene expression matrices prior to pre-processing |
| testFinalEset | Ensure eset is as expected |
| testGEMetaDataPreSummarization | Test gene expression meta-data prior to summarization by gene... |
| testImmuneResponseData | Ensure necessary columns are present in each applicable assay |
| testNoNormEset | Test non-normalized base expression set for reasonable... |
| updateStudyTimepoints | Update study_time_collected for known issues |
| vaccines | Vaccine Mapping Data. |
| write_data_metadata | Write metadata about data to a csv |
| write_processing_metadata | Write a log of processing date to a csv |
| yChromGenes | Y-Chromosome Associated Genes |
