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@@ -78,8 +78,10 @@ remotes::install_github("CSOgroup/CALDER")
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# Usage
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# Usage
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-
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-CALDER works on contact matrices in a three-column `dump` format as generated by the juicer dump command (https://github.com/aidenlab/juicer/wiki/Data-Extraction):
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+CALDER contains three modules: (1) compute chromatin domains; (2) derive their hierarchical organization and obtain sub-compartments; (3) compute nested sub-domains within each compartment domain.
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+<br>
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+<br>
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+CALDER works on contact matrices in a three-column `dump` format as generated by the juicer dump (or straw) command (https://github.com/aidenlab/juicer/wiki/Data-Extraction):
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16050000 16050000 10106.306
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16050000 16050000 10106.306
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16050000 16060000 2259.247
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16050000 16060000 2259.247
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@@ -112,8 +114,6 @@ feature_track = data.table::as.data.table(feature_track)[, c(1:3, 6)]
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chrY 59032416 59032456 0.92023
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chrY 59032416 59032456 0.92023
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chrY 59032457 59032578 0.78875
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chrY 59032457 59032578 0.78875
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-CALDER contains three modules: (1) compute chromatin domains; (2) derive their hierarchical organization and obtain sub-compartments; (3) compute nested sub-domains within each compartment domain.
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-
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### Example one: use contact matrix file in dump format as input
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### Example one: use contact matrix file in dump format as input
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```
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```
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chrs = c(21:22)
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chrs = c(21:22)
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Yuanlong LIU