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... |
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