Data types |
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Tibble for reference sizes. |
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Tibble for intervals. |
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Test if the object is a tbl_genome. |
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Test if the object is a tbl_interval. |
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Coerce objects to tbl_genome. |
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Coerce objects to tbl_intervals. |
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Load data |
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Read BED and related files. |
Read genome files. |
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Read a VCF file. |
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Fetch data from remote databases. |
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Single set operations |
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Cluster neighboring intervals. |
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Identify intervals in a genome not covered by a query. |
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Create flanking intervals from input intervals. |
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Merge overlapping intervals. |
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Partition intervals into elemental intervals |
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Increase the size of input intervals. |
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Adjust intervals by a fixed size. |
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Sort a set of intervals. |
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Multiple set operations |
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Identify closest intervals. |
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Compute coverage of intervals. |
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Identify intersecting intervals. |
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Calculate summaries from overlapping intervals. |
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Subtract two sets of intervals. |
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Identify intervals within a specified distance. |
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Randomizing intervals |
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Generate randomly placed intervals on a genome. |
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Shuffle input intervals. |
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Interval statistics |
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Compute absolute distances between intervals. |
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Compute relative distances between intervals. |
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Fisher's test to measure overlap between two sets of intervals. |
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Calculate the Jaccard statistic for two sets of intervals. |
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Projection test for query interval overlap. |
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Utilities |
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Create intron features. |
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Create transcription start site features. |
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Create 3' UTR features. |
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Create 5' UTR features. |
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Divide intervals into new sub-intervals ("windows"). |
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Convert BED12 to individual exons in BED6. |
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Create example glyphs for valr functions. |
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Select intervals bounded by a genome. |
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Flip strands in intervals. |
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Calculate interval spacing. |
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Provide working directory for valr example files. |