Update README.md

README.md

@@ -148,7 +148,8 @@ CALDER_sub_domains(intermediate_data_file,
 ### Example one:
 ```
 chrs = c(21:22)
-contact_file_dump = as.list(system.file("extdata", sprintf("mat_chr%s_10kb_ob.txt.gz", chrs), package='CALDER'))
+contact_file_dump = as.list(system.file("extdata", sprintf("mat_chr%s_10kb_ob.txt.gz", chrs),
+			package='CALDER'))
 names(contact_file_dump) = chrs
 
 # This will not compute sub-domains, but save the intermediate_data that can be used to compute sub-domains latter on
@@ -166,14 +167,34 @@ CALDER(contact_file_dump=contact_file_dump,
 ### Example two:
 ```
 chrs = c(21:22)
-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
+contact_file_dump = as.list(system.file("extdata", sprintf("mat_chr%s_10kb_ob.txt.gz", chrs),
+			package='CALDER'))
+names(contact_file_dump) = chrs
+contact_tab_dump = lapply(contact_file_dump, data.table::fread)
+
+
+CALDER(contact_tab_dump=contact_tab_dump, 
+			chrs=chrs, 
+			bin_size=10E3,
+			ref_genome='hg19',
+			save_dir=save_dir,
+			save_intermediate_data=FALSE,
+			n_cores=2,
+			sub_domains=FALSE)
+```
+
+### Example three:
+```
+chrs = c(21:22)
+contact_file_dump = as.list(system.file("extdata", sprintf("mat_chr%s_10kb_ob.txt.gz", chrs),
+			package='CALDER'))
+names(contact_file_dump) = chrs
 
 # This will not compute sub-domains, but save the intermediate_data that can be used to compute sub-domains latter on
-CALDER(contact_file_hic=hic_file, 
+CALDER(contact_file_dump=contact_file_dump, 
 			chrs=chrs, 
 			bin_size=10E3,
 			ref_genome=NULL,
-			feature_track=feature_track,
 			save_dir=save_dir,
 			save_intermediate_data=FALSE,
 			n_cores=2,
@@ -181,6 +202,23 @@ CALDER(contact_file_hic=hic_file,
 ```
 
 
+### Example four:
+```
+chrs = c(21:22)
+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
+
+CALDER(contact_file_hic=hic_file, 
+			chrs=chrs, 
+			bin_size=10E3,
+			ref_genome='others',
+			save_dir=save_dir,
+			save_intermediate_data=FALSE,
+			n_cores=2,
+			sub_domains=FALSE)
+```
+
+
+
 
 ### Paramters: