Man pages for kauralasoo/seqUtils

addAssociationPosteriorCalculate posterior probabilities from association summary...
addExpectedPvalueAdd expected p-value for Q-Q plots
addOverlappingPeaksAdd overlapping ATAC peaks to a credible set of QTL variants
addR2FromLeadCalculate R2 between the lead SNP and all other SNPs in the...
annotateCredibleSetAdd ATAC peak annotations to the eQTL credible set
aseDataAddGenotypesTitle Add genotype data to tidy ASE data frame.
calculateCQNNormalize read counts matrix using the cqn method.
calculateEnrichmentCalculate the enrichment of GWAS traits among eQTLs
calculatePairwisePi1Calculate all pairwise Pi1 statistics for a list p-value...
calculatePeakDistanceCaclulate distance between the centres of peak pairs
calculatePermutationPvaluesCalculate emiprical permutation p-values
calculatePi1Calculate Pi1 replicability statistic between two sets of...
calculateTPMNormalise counts matrix using transcripts per million (TPM)...
censorLog2ORCensor log2 odds ratios and their confidence intervals for...
colocMolecularQTLsPerform colocalisation between an single QTL and GWAS summary...
colocMolecularQTLsByRowApplies the colocMolecularQTLs function to each row of the...
colocQtlGWASTest colocalisation between molecular QTL and GWAS summary...
conditionPaletteColour plaette of four colours to represent experimental...
constructCredibleSetConstruct the credible set of associated SNPs for each gene.
constructFastQTLGenePosConstruct gene position data.frame suitable for FastQTL
constructGeneDataFor a given gene_id, extract its expression from...
constructGenotypeTextConstruct matching between minor allele count and genotype...
constructMatrixEQTLCovariatesConvert sample_metadata into a covariates matrix suitable for...
constructMatrixEQTLGenePosConvert gene_metadata table into a gene positions data frame...
constructQTLtoolsGenePosConstruct gene position data.frame suitable for QTLtools
constructVariantRangesConstruct a GRanges obejct corresponding to a cis region...
credibleSetPeakOverlapsIdentify all peak-peak pairs linked by credible sets
dataFrameToGRangesConvert a data frame into a GRanges object
eigenMTExportGenotypesExport genotype data in format suitable for eigenMT
eigenMTExportGenotypesByChrConvert chromosome-wise .gds files into genotype matrices...
eigenMTImportResultsImport eigenMT output file into data frame
estimateVarianceExplainedEstimate propotion of variance explained by each compoent in...
exportDataForRasqualWrite multiple files for RASQUAL onto disk.
extractConditionFromExpressionListExtract samples from expression list based on condition_name...
extractConditionFromSummarizedExperimentExtract samples from SummarizedExperiment based on...
extractGenesFromExpressionListExtract a subset of genes from expression list
extractQTLsFromListExtract all QTLs at a specific FDR level from a list of min...
fastqtlTabixFetchGenesFetch particular genes from tabix indexed FastQTL output...
fastqtlTabixFetchSNPsFetch particular SNPs from tabix indexed Fastqtl output file.
filterHitsR2Filter SNPs based on R2
filterInteractionResultsFilter QTL interaction test results based on RASQUAL effect...
filterOverlapsFilter peak calls based on how many other samples they are...
fimoRelativeEnrichmentCalculate relative motif enrichment in foreground set of...
findGWASOverlapsFind GWAS variants that are in high LD with QTL variants
findMinimalSnpPvaluesFind SNP with minimal p-value per gene.
gdsToMatrixImport genotypes in GDS file to a matrix
getFDRCalculate FDR based on an empirical null distribution
identifyAmbiguousMastersIdentify master peaks that share credible sets with each...
importCredibleSetsImport credible sets from disk and add overlapping peaks to...
importFastQTLTableImport fastQTL output table into R.
importGwasCatalogImport EBI GWAS catalog into R.
importGWASSummaryImport full GWAS summary stats file
importQTLtoolsTableImport QTLtools output table from permutation run into R.
importRasqualTableImport rasqual output table into R
importVariantInformationImport variant information extracted from VCF file into R
loadBroadPeaksImport broadPeak files into a list of GRanges objects.
loadCountsImport featureCounts output table into R.
loadFragmentLengthsImport output files from bedCountFragmentLengths.py script...
loadNarrowPeaksImport narrowPeak files into a list of GRanges objects.
makeMultiplePlotsMake a list of plotEQTL plots.
makeUnionPeaksConstruct the union of list of peak calls and add gene_id and...
matrixeqtlTestInteractionUse MatrixEQTL to test interaction between genotype and two...
plotEQTLMake a boxplot of expression QTL in multiple conditions.
prefilterColocCandidatesPerform a quick pre-filtering between QTLs and GWAS hits to...
prepareFastqtlMatrixAdd gene position to the FastQTL expression matrix
prepareQTLtoolsMatrixAdd gene position to the QTLtools expression matrix
pToZConvert FastQTL p-values into a data frame of z-scores
qtltoolsTabixFetchPhenotypesFetch particular genes from tabix indexed QTLtools output...
quantifyMotifDisruptionEstimate how much PWM binding score is altered by the SNP
quantifyMultipleMotifsApplies quantifyMotifDisruption to a list of motifs
quantifyMultipleVariantsApplies quantifyMultipleMotifs to a data frame of peak and...
quantileNormaliseVectorForce a vector of values into standard normal distribution
rankAtacSummariesAdd gene_id and gene_name to atac hits and rank them by...
runMatrixEQTLA wrapper around MatrixeQTL
saveFastqtlMatricesSave a list of matrices into a suitable format for FastQTL
savePEERDataSave list of expression matrices in a format suitable for...
savePlotsSave a list of ggplot2 plots into a folder
scanTabixDataFrameA general function to quickly import tabix indexed...
splitIntoBatchesSplit vector of n elements into batches
subsampleFisherTestPerform Fisher's Exact test when sample is a subsample of a...
tabixFetchGWASSummaryImport a specific region from a tabix-indexed GWAS summary...
tbl_df2Convert bioconductor DataFrame object into tibble
testColocWrapper around coloc.abf to directly work with tidy data...
testInteractionTest for interaction between genotype and condition using...
testInteractionLme4Test for interaction between genotype and condition using...
testThreewayInteractionTest for threeway interactions between two features, genotype...
tibbleToNamedMatrixConvert a data frame with an id column into a matrix with row...
tidyGenotypeMatrixConvert genotype matrix from gdsToMatrix into a tidy data...
tidyVectorConvert named vector into a tidy data_frame.
varianceExplainedCalculate the proportion of variance explaned by different...
wiggleplotrConstructMetadataConstruct metadata data frame for wiggleplotr
zToLDCalculate LD matrix based on a data frame of z-scores and...
kauralasoo/seqUtils documentation built on Oct. 31, 2017, 11:36 p.m.