Files in kauralasoo/eQTLUtils

R/GDSArray_helpers.R R/SummarizedExperiment_QC_norm.R R/SummarizedExperiment_helpers.R R/array_qc_utils.R R/eQTLUtils-package.r R/finemapping.R R/genotype_dose_matrix.R R/import_data.R R/matrix_operations.R R/pop_assign.R R/qtl_QTLTools.R R/qtltools_normalisation_wrappers.R R/quant_leafcutter.R R/quant_txrevise.R R/rna_qc_utils.R man/array_Boxplot.Rd man/array_CalculateSexQCDataFrame.Rd man/array_PlotMDS.Rd man/array_PlotSexQC.Rd man/array_RemoveBatch2.Rd man/array_normaliseSE2.Rd man/array_plotPCA.Rd man/assign_populations.Rd man/calculateMDSMatrix.Rd man/calculatePCAMatrix.Rd man/calculateSexQCDataFrame.Rd man/calculateTranscriptUsage.Rd man/calculate_rna_qc_matrices.Rd man/checkCisVariants.Rd man/convertSEtoQTLtools.Rd man/estimateMedianTPM.Rd man/extractGenotypeMatrixFromDosage.Rd man/extractGenotypeMatrixFromGDS.Rd man/extractPhentypeFromSE.Rd man/extractVariantGenotypeFromGDS.Rd man/filterSummarizedExperiment.Rd man/generate_distance_matrix.Rd man/importBiomartMetadata.Rd man/importQTLtoolsPermRes.Rd man/importQTLtoolsTable.Rd man/importTxreviseCounts.Rd man/importVariantInformation.Rd man/importVariantInformationFromGDS.Rd man/leafcutterAnnotateIntrons.Rd man/log2_transform.Rd man/makeSummarizedExperimentFromCountMatrix.Rd man/mbvFindBestMatch.Rd man/mbvImportData.Rd man/normaliseSE_cqn.Rd man/normaliseSE_quantile.Rd man/normaliseSE_ratios.Rd man/normaliseSE_tpm.Rd man/plotMDSAnalysis.Rd man/plotMDSFromMatrix.Rd man/plotPCAAnalysis.Rd man/plotPCAFromMatrix.Rd man/plotSexQC.Rd man/plotSexQCFromMatrix.Rd man/plot_mbv_results.Rd man/plot_rna_qc_all.Rd man/qtltoolsPrepareSE.Rd man/qtltoolsTabixFetchPhenotypes.Rd man/quantileNormaliseCols.Rd man/quantileNormaliseRows.Rd man/quantileNormaliseVector.Rd man/reassign_populations.Rd man/reformatPhenotypeId.Rd man/replaceNAsWithRowMeans.Rd man/saveQTLToolsMatrices.Rd man/scanTabixDataFrame.Rd man/studySEtoCountMatrices.Rd man/studySEtoQTLTools.Rd man/subsetSEByColumnValue.Rd man/transformSE_PCA.Rd