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@@ -148,7 +148,8 @@ CALDER_sub_domains(intermediate_data_file,
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### Example one:
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```
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chrs = c(21:22)
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-contact_file_dump = as.list(system.file("extdata", sprintf("mat_chr%s_10kb_ob.txt.gz", chrs), package='CALDER'))
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+contact_file_dump = as.list(system.file("extdata", sprintf("mat_chr%s_10kb_ob.txt.gz", chrs),
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+ package='CALDER'))
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names(contact_file_dump) = chrs
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# This will not compute sub-domains, but save the intermediate_data that can be used to compute sub-domains latter on
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@@ -166,14 +167,34 @@ CALDER(contact_file_dump=contact_file_dump,
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### Example two:
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```
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chrs = c(21:22)
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-hic_file = 'HMEC_combined_30.hic' ## can be downloaded from https://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_HMEC_combined_30.hic
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+contact_file_dump = as.list(system.file("extdata", sprintf("mat_chr%s_10kb_ob.txt.gz", chrs),
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+ package='CALDER'))
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+names(contact_file_dump) = chrs
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+contact_tab_dump = lapply(contact_file_dump, data.table::fread)
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+
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+
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+CALDER(contact_tab_dump=contact_tab_dump,
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+ chrs=chrs,
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+ bin_size=10E3,
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+ ref_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=FALSE)
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+```
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+
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+### Example three:
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+```
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+chrs = c(21:22)
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+contact_file_dump = as.list(system.file("extdata", sprintf("mat_chr%s_10kb_ob.txt.gz", chrs),
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+ package='CALDER'))
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+names(contact_file_dump) = chrs
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# This will not compute sub-domains, but save the intermediate_data that can be used to compute sub-domains latter on
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-CALDER(contact_file_hic=hic_file,
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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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ref_genome=NULL,
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- feature_track=feature_track,
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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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@@ -181,6 +202,23 @@ CALDER(contact_file_hic=hic_file,
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```
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+### Example four:
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+```
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+chrs = c(21:22)
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+hic_file = 'HMEC_combined_30.hic' ## can be downloaded from https://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_HMEC_combined_30.hic
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+
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+CALDER(contact_file_hic=hic_file,
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+ chrs=chrs,
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+ bin_size=10E3,
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+ ref_genome='others',
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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=FALSE)
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+```
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+
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+
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+
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### Paramters:
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Yuanlong LIU