Package index
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adjustCovariateMatrix() - Use of matrix functions to adjust data via linear model
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assignRegion2GeneDirection() - The results from all correlations are used to help assign direction using correlations that have a significant nominal pvalue
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categorizeAndAnnotateCorrelationResults() - Annotation of genes that are significant and provide some additional downstream information for interpreting linked networks
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corWithDistalPeak() - Iteration of correlations between distal peaks and other peaks residing near it with significant relationships with said gene
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corWithDistalPeak_wrapper() - Wrapper function for corWithDistalPeak to iterate through the correlations
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correlateByChromosome() - A wrapper function to carry out correlations in smaller chunks to help save on memory
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createPeak2GeneObjects() - Create Peak-Gene Links Set up genomicranges objects for the data included in the correlation analysis. Data matrices must have unique feature IDs.
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editCorResFields() - Annotation of significant promoter peak information
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formatMatrixForCorrelation() - Format input
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gene_counts - Example Gene Counts
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matrixCorrelation() - Correlation of two matrices for more efficient calculations
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peak_counts - Example Peak Counts
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processCorrelations() - Process correlation results