Man pages for aksenia/SeeCiTe
Assess the quality of and visualize array CNV callset for trios
| analyzeSignalConcordance | SeeCiTe analysis of BAF and LRR in candidate offspring CNV... |
| analyzeSignalConcordanceSingle | Patial SeeCiTe analysis of BAF and LRR in candidate CNV... |
| calcShift | Create a decile plot and a scatter for CNV versus flanking... |
| classifyBAF | Cluster BAF values using given cluster centers, a helper... |
| classifySingles | Main function that uses prepared summary statistics to... |
| classifyTrios | Main function that uses prepared summary statistics to... |
| clusterBAF | Cluster BAF values using given cluster centers, helper... |
| decodeHMMstates | Create a table mapping PennCNV HMM states to copy numbers |
| extractInheritance | Annotate original PennCNV trio data table with inheritance... |
| makePythonCommands | Create commands to run helper python scripts that automate... |
| mapTriostate | Link inheritance status and original trio state as well as... |
| pipe | Pipe operator |
| plotCohort | Write the pdf files with the visualisations of local CNV SNP... |
| plotRawTrio | Visualize local CNV SNP data and key summary statistics for a... |
| plotSingle | Visualize local CNV SNP data and key summary statistics for a... |
| prepareClass | Prepare data summaries for final classifications, a helper... |
| prepareClassSingle | Prepare data summaries for final classifications, a helper... |
| readInputs | Load and combine multiple input files |
| readPennTrioFormat | Load PennCNV trio adapted file into R. Expects the coding... |
| readPennTrioOriginal | Load PennCNV trio file in original format as supplied by... |
| readSingle | Load and format data for single sample processing |
| runAnalyzeSignal | A wrapper around analyzeSignalConcordance(Single) function to... |
| runExtractInheritance | Annotate original PennCNV trio data table with inheritance... |
| stabilizeDistr | Remove outliers in the CNV locus LRR values, a helper... |
| statusFromTriostate | Extract inheritance status from penn trio string collapsing... |
| testLRRDistributions | Apply a row of statistical tests to LRR distribtuions in CNV... |
| testLRRDistributionsSingle | Apply a row of statistical tests to LRR distribuions in CNV... |
| writeSeecite | Write the CNV files with SeeCiTe assessment and all summary... |
