API for kauralasoo/eQTLUtils
| Global functions | |
|---|---|
| array_Boxplot | Man page Source code |
| array_CalculateSexQCDataFrame | Man page Source code |
| array_PlotMDS | Man page Source code |
| array_PlotSexQC | Man page Source code |
| array_RemoveBatch2 | Man page Source code |
| array_filterSE_gene_types | Source code |
| array_normaliseSE2 | Man page Source code |
| array_plotPCA | Man page Source code |
| assign_populations | Man page Source code |
| calculateMDSMatrix | Man page Source code |
| calculateMean | Source code |
| calculatePCAMatrix | Man page Source code |
| calculatePairwiseCSMetrics | Source code |
| calculateSexQCDataFrame | Man page Source code |
| calculateTranscriptUsage | Man page Source code |
| calculate_rna_qc_matrices | Man page Source code |
| checkCisVariants | Man page Source code |
| constructTxreviseRowData | Source code |
| convertSEtoQTLtools | Man page Source code |
| estimateMedianTPM | Man page Source code |
| extractGeneMetadataFromBiomartFile | Source code |
| extractGenotypeMatrixFromDosage | Man page Source code |
| extractGenotypeMatrixFromGDS | Man page Source code |
| extractPhentypeFromSE | Man page Source code |
| extractVariantGenotypeFromGDS | Man page Source code |
| filterSE_expressedGenes | Source code |
| filterSummarizedExperiment | Man page Source code |
| generate_distance_matrix | Man page Source code |
| importBiomartMetadata | Man page Source code |
| importQTLtoolsNominalTable | Source code |
| importQTLtoolsPCA | Source code |
| importQTLtoolsPermRes | Man page Source code |
| importQTLtoolsTable | Man page Source code |
| importTxreviseCounts | Man page Source code |
| importVariantInformation | Man page Source code |
| importVariantInformationFromGDS | Man page Source code |
| leafcutterAnnotateIntrons | Man page Source code |
| leafcutterConstructMeta | Source code |
| log2_transform | Man page Source code |
| makeFeatureCountsSummarizedExperiment | Source code |
| makeSummarizedExperiment | Source code |
| makeSummarizedExperimentFromCountMatrix | Man page Source code |
| mbvFindBestMatch | Man page Source code |
| mbvImportData | Man page Source code |
| mergeCountsSEs | Source code |
| normaliseSE_cqn | Man page Source code |
| normaliseSE_quantile | Man page Source code |
| normaliseSE_ratios | Man page Source code |
| normaliseSE_tpm | Man page Source code |
| plotMDSAnalysis | Man page Source code |
| plotMDSFromMatrix | Man page Source code |
| plotPCAAnalysis | Man page Source code |
| plotPCAFromMatrix | Man page Source code |
| plotSexQC | Man page Source code |
| plotSexQCFromMatrix | Man page Source code |
| plot_mbv_results | Man page Source code |
| plot_rna_qc_all | Man page Source code |
| qtltoolsPrepareSE | Man page Source code |
| qtltoolsTabixFetchPhenotypeVariantPairs | Source code |
| qtltoolsTabixFetchPhenotypes | Man page Source code |
| quantileNormaliseCols | Man page Source code |
| quantileNormaliseMatrix | Source code |
| quantileNormaliseRows | Man page Source code |
| quantileNormaliseVector | Man page Source code |
| reassign_populations | Man page Source code |
| reformatPhenotypeId | Man page Source code |
| removeGeneVersion | Source code |
| replaceNAsWithRowMeans | Man page Source code |
| saveQTLToolsMatrices | Man page Source code |
| scanTabixDataFrame | Man page Source code |
| studySEtoCountMatrices | Man page |
| studySEtoQTLTools | Man page Source code |
| subsetSEByColumnValue | Man page Source code |
| transformSE_PCA | Man page Source code |
| zScoreNormalize | Source code |
