Browse Source

Update README.md

Yuanlong LIU 2 years ago
parent
commit
48662bd3fd
1 changed files with 2 additions and 2 deletions
  1. 2 2
      README.md

+ 2 - 2
README.md

@@ -201,7 +201,7 @@ names(contact_file_dump) = chrs
 CALDER(contact_file_dump=contact_file_dump, 
 			chrs=chrs, 
 			bin_size=10E3,
-			genome=others,
+			genome='others',
 			save_dir=save_dir,
 			feature_track=feature_track,
 			save_intermediate_data=FALSE,
@@ -219,7 +219,7 @@ CALDER(contact_file_dump=contact_file_dump,
 | **contact_file_dump**                |A list of contact files in dump format, named by `chrs`. Each contact file stores the contact information of the corresponding `chr`. Only one of `contact_file_dump`, `contact_tab_dump`, `contact_file_hic` should be provided
 | **contact_tab_dump**                | A list of contact table in dump format, named by `chrs`, stored as an R object. Only one of `contact_file_dump`, `contact_tab_dump`, `contact_file_hic` should be provided
 | **contact_file_hic**                | A hic file generated by Juicer tools. It should contain all chromosomes in `chrs`. Only one of `contact_file_dump`, `contact_tab_dump`, `contact_file_hic` should be provided
-| **genome**                | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default). These compartments will be used as reference compartments for optimized bin_size selection. If `genome = others`, a `feature_track` should be provided (see below) and no optimized bin_size selection will be performed 
+| **genome**                | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default). These compartments will be used as reference compartments for optimized bin_size selection. If `genome = 'others'`, a `feature_track` should be provided (see below) and no optimized bin_size selection will be performed 
 | **save_dir**             | the directory to be created for saving outputs
 | **bin_size**         | The bin_size (resolution) to run CALDER. `bin_size` should be consistent with the data resolution in `contact_file_dump` or `contact_tab_dump` if these files are provided as input, otherwise `bin_size` should exist in `contact_file_hic`. Recommended `bin_size` is between **10000 to 100000**
 | **single_binsize_only**     |  logical. If TRUE, CALDER will compute compartments only using the bin_size specified by the user and not do bin size optimization