Man pages for kauralasoo/seqUtils
| addAssociationPosterior | Calculate posterior probabilities from association summary... |
| addExpectedPvalue | Add expected p-value for Q-Q plots |
| addOverlappingPeaks | Add overlapping ATAC peaks to a credible set of QTL variants |
| addR2FromLead | Calculate R2 between the lead SNP and all other SNPs in the... |
| annotateCredibleSet | Add ATAC peak annotations to the eQTL credible set |
| aseDataAddGenotypes | Title Add genotype data to tidy ASE data frame. |
| calculateCQN | Normalize read counts matrix using the cqn method. |
| calculateEnrichment | Calculate the enrichment of GWAS traits among eQTLs |
| calculatePairwisePi1 | Calculate all pairwise Pi1 statistics for a list p-value... |
| calculatePeakDistance | Caclulate distance between the centres of peak pairs |
| calculatePermutationPvalues | Calculate emiprical permutation p-values |
| calculatePi1 | Calculate Pi1 replicability statistic between two sets of... |
| calculateTPM | Normalise counts matrix using transcripts per million (TPM)... |
| censorLog2OR | Censor log2 odds ratios and their confidence intervals for... |
| colocMolecularQTLs | Perform colocalisation between an single QTL and GWAS summary... |
| colocMolecularQTLsByRow | Applies the colocMolecularQTLs function to each row of the... |
| colocQtlGWAS | Test colocalisation between molecular QTL and GWAS summary... |
| conditionPalette | Colour plaette of four colours to represent experimental... |
| constructCredibleSet | Construct the credible set of associated SNPs for each gene. |
| constructFastQTLGenePos | Construct gene position data.frame suitable for FastQTL |
| constructGeneData | For a given gene_id, extract its expression from... |
| constructGenotypeText | Construct matching between minor allele count and genotype... |
| constructMatrixEQTLCovariates | Convert sample_metadata into a covariates matrix suitable for... |
| constructMatrixEQTLGenePos | Convert gene_metadata table into a gene positions data frame... |
| constructQTLtoolsGenePos | Construct gene position data.frame suitable for QTLtools |
| constructVariantRanges | Construct a GRanges obejct corresponding to a cis region... |
| credibleSetPeakOverlaps | Identify all peak-peak pairs linked by credible sets |
| dataFrameToGRanges | Convert a data frame into a GRanges object |
| eigenMTExportGenotypes | Export genotype data in format suitable for eigenMT |
| eigenMTExportGenotypesByChr | Convert chromosome-wise .gds files into genotype matrices... |
| eigenMTImportResults | Import eigenMT output file into data frame |
| estimateVarianceExplained | Estimate propotion of variance explained by each compoent in... |
| exportDataForRasqual | Write multiple files for RASQUAL onto disk. |
| extractConditionFromExpressionList | Extract samples from expression list based on condition_name... |
| extractGenesFromExpressionList | Extract a subset of genes from expression list |
| extractQTLsFromList | Extract all QTLs at a specific FDR level from a list of min... |
| fastqtlTabixFetchGenes | Fetch particular genes from tabix indexed FastQTL output... |
| fastqtlTabixFetchSNPs | Fetch particular SNPs from tabix indexed Fastqtl output file. |
| filterHitsR2 | Filter SNPs based on R2 |
| filterInteractionResults | Filter QTL interaction test results based on RASQUAL effect... |
| filterOverlaps | Filter peak calls based on how many other samples they are... |
| fimoRelativeEnrichment | Calculate relative motif enrichment in foreground set of... |
| findGWASOverlaps | Find GWAS variants that are in high LD with QTL variants |
| findMinimalSnpPvalues | Find SNP with minimal p-value per gene. |
| gdsToMatrix | Import genotypes in GDS file to a matrix |
| getFDR | Calculate FDR based on an empirical null distribution |
| identifyAmbiguousMasters | Identify master peaks that share credible sets with each... |
| importCredibleSets | Import credible sets from disk and add overlapping peaks to... |
| importFastQTLTable | Import fastQTL output table into R. |
| importGwasCatalog | Import EBI GWAS catalog into R. |
| importGWASSummary | Import full GWAS summary stats file |
| importQTLtoolsTable | Import QTLtools output table from permutation run into R. |
| importRasqualTable | Import rasqual output table into R |
| importVariantInformation | Import variant information extracted from VCF file into R |
| loadBroadPeaks | Import broadPeak files into a list of GRanges objects. |
| loadCounts | Import featureCounts output table into R. |
| loadFragmentLengths | Import output files from bedCountFragmentLengths.py script... |
| loadNarrowPeaks | Import narrowPeak files into a list of GRanges objects. |
| makeMultiplePlots | Make a list of plotEQTL plots. |
| makeUnionPeaks | Construct the union of list of peak calls and add gene_id and... |
| matrixeqtlTestInteraction | Use MatrixEQTL to test interaction between genotype and two... |
| plotEQTL | Make a boxplot of expression QTL in multiple conditions. |
| prefilterColocCandidates | Perform a quick pre-filtering between QTLs and GWAS hits to... |
| prepareFastqtlMatrix | Add gene position to the FastQTL expression matrix |
| prepareQTLtoolsMatrix | Add gene position to the QTLtools expression matrix |
| pToZ | Convert FastQTL p-values into a data frame of z-scores |
| qtltoolsTabixFetchPhenotypes | Fetch particular genes from tabix indexed QTLtools output... |
| quantifyMotifDisruption | Estimate how much PWM binding score is altered by the SNP |
| quantifyMultipleMotifs | Applies quantifyMotifDisruption to a list of motifs |
| quantifyMultipleVariants | Applies quantifyMultipleMotifs to a data frame of peak and... |
| quantileNormaliseVector | Force a vector of values into standard normal distribution |
| rankAtacSummaries | Add gene_id and gene_name to atac hits and rank them by... |
| runMatrixEQTL | A wrapper around MatrixeQTL |
| saveFastqtlMatrices | Save a list of matrices into a suitable format for FastQTL |
| savePEERData | Save list of expression matrices in a format suitable for... |
| savePlots | Save a list of ggplot2 plots into a folder |
| saveQTLToolsMatrices | Save a list of matrices into a suitable format for FastQTL |
| scanTabixDataFrame | A general function to quickly import tabix indexed... |
| splitIntoBatches | Split vector of n elements into batches |
| subsampleFisherTest | Perform Fisher's Exact test when sample is a subsample of a... |
| tabixFetchGWASSummary | Import a specific region from a tabix-indexed GWAS summary... |
| tbl_df2 | Convert bioconductor DataFrame object into tibble |
| testColoc | Wrapper around coloc.abf to directly work with tidy data... |
| testInteraction | Test for interaction between genotype and condition using... |
| testInteractionLme4 | Test for interaction between genotype and condition using... |
| testThreewayInteraction | Test for threeway interactions between two features, genotype... |
| tibbleToNamedMatrix | Convert a data frame with an id column into a matrix with row... |
| tidyGenotypeMatrix | Convert genotype matrix from gdsToMatrix into a tidy data... |
| tidyVector | Convert named vector into a tidy data_frame. |
| varianceExplained | Calculate the proportion of variance explaned by different... |
| wiggleplotrConstructMetadata | Construct metadata data frame for wiggleplotr |
| zToLD | Calculate LD matrix based on a data frame of z-scores and... |
