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@@ -36,15 +36,20 @@ Note that this strategy is currently only available for `hg19`, `hg38`, `mm9` an
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Although CALDER was mainly tested on human and mouse dataset, it can be applied on dataset from other genomes. One additional information is required in such case: a `feature_track` that is presumably positively correlated with compartment score (thus higher values in A than in B compartment). This information will be used for correctly determing the `A/B` direction. Some suggested tracks are gene density, H3K27ac, H3K4me1, H3K4me2, H3K4me3, H3K36me3 (or negative transform of H3K9me3) signals. Note that this information will not alter the hierarchical compartment/TAD structure, and can come from any external study with matched genome.
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- 16050000 16050000 10106.306
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- 16050000 16060000 2259.247
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- 16060000 16060000 7748.551
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- 16050000 16070000 1251.3663
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- 16060000 16070000 4456.1245
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- 16070000 16070000 4211.7393
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- 16050000 16080000 522.0705
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- 16060000 16080000 983.1761
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- 16070000 16080000 1996.749
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+rtracklayer
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+
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+chr start end score
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+chr1 1 534178 0
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+chr1 534179 534353 2.80512
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+chr1 534354 572399 0
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+chr1 572400 572574 2.80512
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+chr1 572575 628400 0
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+… … … …
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+chrY 59031457 59032403 0
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+chrY 59032404 59032413 0.92023
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+chrY 59032414 59032415 0.96625
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+chrY 59032416 59032456 0.92023
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+chrY 59032457 59032578 0.78875
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...
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# Installation
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Yuanlong LIU