Man pages for kauralasoo/eQTLUtils

array_BoxplotGenerate Boxplot QC Plot for n random samples
array_CalculateSexQCDataFrameGenerate Sex dependent QC DataFrame.
array_normaliseSENormalise microarray data using lumiN function
array_PlotMDSGenerate MDS QC Plot
array_plotPCAGenerate PCA QC Plot
array_PlotSexQCGenerate Sex dependent QC Plot.
array_RemoveBatchAdjust for batch effects using limma removeBatchEffect
calculateMDSMatrixGenerate MDS Matrix for SummarizedExperiment
calculatePCAMatrixGenerate PCA Matrix for SummarizedExperiment
calculateSexQCDataFrameGenerate Sex dependent QC DataFrame.
checkCisVariantsRemove phenotypes from SummarizedExperiments that do not have...
convertSEtoQTLtoolsConvert SummarizedExperiment object into a bed file suitable...
importQTLtoolsTableImport QTLtools output table from permutation run into R.
importVariantInformationImport variant information extracted from VCF file into R
log2_transformLog2 transform intensity values (same approach as in function...
mbvFindBestMatchPost-process QTLTools mbv results to find the best matching...
normaliseSE_quantileQuantile normalise SummarizedExperiment by rows
plotMDSAnalysisGenerate MDS QC Plot for different cell types
plotPCAAnalysisGenerate PCA QC Plot for different cell types
plotSexQCGenerate Sex dependent QC Plot.
qtltoolsTabixFetchPhenotypesFetch particular genes from tabix indexed QTLtools output...
quantileNormaliseVectorForce a vector of values into standard normal distribution
saveQTLToolsMatricesSave a list of matrices into a suitable format for QTLTools
scanTabixDataFrameA general function to quickly import tabix indexed...
subsetSEByColumnValueExtract a subset of the data from a SummarizedExperiment...
kauralasoo/eQTLUtils documentation built on Nov. 28, 2018, 4:14 p.m.