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@@ -114,7 +114,7 @@ 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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-### Example one: use contact matrix file in dump format as input
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+### Example usage 1: 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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@@ -123,7 +123,7 @@ contact_file_dump = as.list(system.file("extdata", sprintf("mat_chr%s_10kb_ob.tx
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package='CALDER'))
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package='CALDER'))
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names(contact_file_dump) = chrs
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names(contact_file_dump) = chrs
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-# Run CALDER to compute compartments
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+# Run CALDER to compute compartments but not nested sub-domains
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CALDER(contact_file_dump=contact_file_dump,
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CALDER(contact_file_dump=contact_file_dump,
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chrs=chrs,
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chrs=chrs,
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bin_size=10E3,
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bin_size=10E3,
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@@ -132,6 +132,16 @@ CALDER(contact_file_dump=contact_file_dump,
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save_intermediate_data=FALSE,
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save_intermediate_data=FALSE,
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n_cores=2,
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n_cores=2,
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sub_domains=FALSE)
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sub_domains=FALSE)
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+
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+# Run CALDER to compute compartments and nested sub-domains / will take more time
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+CALDER(contact_file_dump=contact_file_dump,
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+ chrs=chrs,
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+ bin_size=10E3,
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+ genome='hg19',
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+ save_dir=save_dir,
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+ save_intermediate_data=FALSE,
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+ n_cores=2,
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+ sub_domains=TRUE)
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```
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```
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### Example two: use an R list of contact matrices in dump format as input
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### Example two: use an R list of contact matrices in dump format as input
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Yuanlong LIU