Man pages for kauralasoo/eQTLUtils
| array_Boxplot | Generate Boxplot QC Plot for n random samples |
| array_CalculateSexQCDataFrame | Generate Sex dependent QC DataFrame. |
| array_normaliseSE2 | Normalise microarray data using lumiN function |
| array_PlotMDS | Generate MDS QC Plot |
| array_plotPCA | Generate PCA QC Plot |
| array_PlotSexQC | Generate Sex dependent QC Plot. |
| array_RemoveBatch2 | Adjust for batch effects using limma removeBatchEffect |
| assign_populations | Assigns populations using distance matrix from... |
| calculateMDSMatrix | Generate MDS Matrix for SummarizedExperiment |
| calculatePCAMatrix | Generate PCA Matrix for SummarizedExperiment |
| calculate_rna_qc_matrices | Export RNA QC (PCA, MDS, Sex) matrices |
| calculateSexQCDataFrame | Generate Sex dependent QC DataFrame. |
| calculateTranscriptUsage | Calculate the transcript usage |
| checkCisVariants | Remove phenotypes from SummarizedExperiments that do not have... |
| convertSEtoQTLtools | Convert SummarizedExperiment object into a bed file suitable... |
| estimateMedianTPM | Estimate median TPM for each gene in each sample group of a... |
| extractGenotypeMatrixFromDosage | Extract genotype matrix from a dosage file generated by... |
| extractGenotypeMatrixFromGDS | Extract a genotype matrix corresponding to a specific genomic... |
| extractPhentypeFromSE | Extract a single phenotype from a SummarizedExperiment... |
| extractVariantGenotypeFromGDS | Extract genotypes of a single genetic variant from the GDS... |
| filterSummarizedExperiment | Filter a Summarized Experiment according to provided... |
| generate_distance_matrix | Generate distance matrix of genotype samples using PC... |
| importBiomartMetadata | Import transcript metadata from biomart web export |
| importQTLtoolsPermRes | Import QTLtools output table from permutation run v2 into R. |
| importQTLtoolsTable | Import QTLtools output table from permutation run into R. |
| importTxreviseCounts | Read and merge the TxRevise count matrices |
| importVariantInformation | Import variant information extracted from VCF file into R |
| importVariantInformationFromGDS | Import variant information from GDS file |
| leafcutterAnnotateIntrons | Annotate leafcutter introns with gene metadata |
| log2_transform | Log2 transform intensity values (same approach as in function... |
| makeSummarizedExperimentFromCountMatrix | Make Summarized Experiment object from raw or normalised... |
| mbvFindBestMatch | Post-process QTLTools mbv results to find the best matching... |
| mbvImportData | Import MBV output files for all samples in a studt |
| normaliseSE_cqn | Normalises the assay of SE with cqn method |
| normaliseSE_quantile | Quantile normalise SummarizedExperiment by rows |
| normaliseSE_ratios | normaliseSE_ratios |
| normaliseSE_tpm | Normalises the assay of SE with TPM method |
| plot_mbv_results | Generate MBV_results plots |
| plotMDSAnalysis | Generate MDS QC Plot for different cell types |
| plotMDSFromMatrix | Generate MDS QC Plot from PCA Matrix |
| plotPCAAnalysis | Generate PCA QC Plot for different cell types |
| plotPCAFromMatrix | Generate PCA QC Plot from PCA Matrix |
| plot_rna_qc_all | Generate RNA QC (PCA, MDS, Sex) plots |
| plotSexQC | Generate Sex dependent QC Plot. |
| plotSexQCFromMatrix | Generate Sex dependent QC Plot. |
| qtltoolsPrepareSE | Normalise phenotype SummarisedExperiment object for QTL... |
| qtltoolsTabixFetchPhenotypes | Fetch particular genes from tabix indexed QTLtools output... |
| quantileNormaliseCols | Perform inverse normal transformation on the columns of a... |
| quantileNormaliseRows | Perform inverse normal transformation on the rows of a matrix |
| quantileNormaliseVector | Force a vector of values into standard normal distribution |
| reassign_populations | Reassigns already assigned populations according to new... |
| reformatPhenotypeId | Reformat phenotype IDs according to quantification method |
| replaceNAsWithRowMeans | replaceNAsWithRowMeans |
| saveQTLToolsMatrices | Save a list of matrices into a suitable format for QTLTools |
| scanTabixDataFrame | A general function to quickly import tabix indexed... |
| studySEtoCountMatrices | Split study SummarizedExperiment object into invidiual input... |
| studySEtoQTLTools | Split study SummarizedExperiment object into invidiual input... |
| subsetSEByColumnValue | Extract a subset of the data from a SummarizedExperiment... |
| transformSE_PCA | Quantile normalise SummarizedExperiment by rows |
