bug fixed

R/CALDER_hierarchy_v2.R

@@ -237,7 +237,6 @@
 	        p_thresh = ifelse(bin_size2look < 40000, 0.05, 1)
 	        window.sizes = 3
 	        compartments = vector("list", 2)
-	        chr_name = paste0("chr", chr)
 
 	        cat('>>>> Begin compute compartment domains and their hierachy at:', as.character(Sys.time()), '\n', file=log_file, append=TRUE)
 	        cat('\r', '>>>> Begin compute compartment domains and their hierachy at:', as.character(Sys.time()))

R/compartment_data_generation_fun.R

@@ -39,7 +39,7 @@
 
 			## try different normalization to get available dataset
 
-			contact_mat_raw = try(strawr::dump("KR", contact_file_hic, as.character(chr2query), as.character(chr2query), "BP", bin_size_input))
+			contact_mat_raw = try(strawr::straw("KR", contact_file_hic, as.character(chr2query), as.character(chr2query), "BP", bin_size_input))
 			if(class(contact_mat_raw)=='try-error' | (class(contact_mat_raw)!='try-error' & nrow(na.omit(contact_mat_raw)) < 100)) contact_mat_raw = try(strawr::dump("VC_SQRT", contact_file_hic, as.character(chr2query), as.character(chr2query), "BP", bin_size_input))
 			if(class(contact_mat_raw)=='try-error' | (class(contact_mat_raw)!='try-error' & nrow(na.omit(contact_mat_raw)) < 100)) contact_mat_raw = try(strawr::dump("VC", contact_file_hic, as.character(chr2query), as.character(chr2query), "BP", bin_size_input))
 			if(class(contact_mat_raw)=='try-error' | (class(contact_mat_raw)!='try-error' & nrow(na.omit(contact_mat_raw)) < 100)) stop(sprintf('Your provided hic file does not contain information given the bin_size=%s and any of the normalization method KR/VC/VC_SQRT', bin_size_input))