Package index
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XqtlExperiment-class - extend RangedSummarizedExperiment to include genotype calls in a GRanges
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XqtlExperiment() - XqtlExperiment constructor
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add_scores() - internal function to combine new xQTL test results with existing XqtlExperiment instance
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bind_Zs() - compute Z-statistics for xQTL association and bind them to the input x-ome+genome XqtlExperiment
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countGenotypes() - Count genotypes across samples for each variant
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countGenotypesVectorized() - More efficient vectorized version for large datasets
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demo_vcf() - provide path to a demonstration VCF file
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example_tensorQTL() - produce arrow dataset with tensorQTL cis example output
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fastLmMany_R() - Fit multiple linear models with common design matrix
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filterCalls() - filter the call component of an XqtlExperiment
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filterVcfByGenotypeCounts() - Filter VCF to variants with minimum counts in each genotype group
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filterVcfMultipleCriteria() - Filter VCF with multiple criteria
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getCalls() - getter for genotype calls
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getGenotypeSummary() - Get genotype summary statistics
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get_tensor_example_path() - operate with BiocFileCache to retrieve zip file of tensorQTL output
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geuv19 - a RangedSummarizedExperiment with data from GeuvadisTranscriptExpr
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geuv19_samples - data frame with sample information for geuv19
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geuv19xse - a RangedSummarizedExperiment with data from GeuvadisTranscriptExpr, in XqtlExperiment format
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maf() - compute putative minor allele frequency for XqtlExperiment
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mageSE_19 - SummarizedExperiment from MAGE
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minorAlleleCounts() - produce data.frame with minor allele counts in a region, from VCF
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show(<XqtlExperiment>) - present concise view of XqtlExperiment
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tens445 - SummarizedExperiment with example data from tensorQTL, with 445 individuals from the GEUVADIS project
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tiles38 - a GRanges tiling GRCh38
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viz_stats() - produce a plotly display of statistics of xQTL association
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zs4manyYs() - use procedure tailored to multiple responses for a fixed design matrix