ScRepLoading¶

Load the single cell TCR/BCR data into a scRepertoire compatible object

This process loads the single cell TCR/BCR data into a scRepertoire (>= v2.0.8, < v2.3.2) compatible object. Later, scRepertoire::combineExpression can be used to combine the expression data with the TCR/BCR data.

For the data path specified at TCRData/BCRData in the input file (in.metafile), will be used to find the TCR/BCR data files and scRepertoire::loadContigs() will be used to load the data.

A directory can be specified in TCRData/BCRData, then scRepertoire::loadContigs() will be used directly to load the data from the directory. Otherwise if a file is specified, it will be symbolically linked to a directory for scRepertoire::loadContigs() to load.
Note that when the file name can not be recognized by scRepertoire::loadContigs(), envs.format must be set for the correct format of the data.

Input¶

• metafile: The meta data of the samples A tab-delimited file Two columns are required:
  
  • Sample to specify the sample names.
    
  • TCRData/BCRData to assign the path of the data to the samples, and this column will be excluded as metadata.
    

Output¶

• outfile: Default: {{in.metafile | stem}}.scRep.qs.
  The scRepertoire compatible object in qs/qs2 format

Environment Variables¶

• type (choice): Default: auto.
  The type of the data to load.
  
  • TCR: T cell receptor data
  • BCR: B cell receptor data
  • auto: Automatically detect the type from the metadata.
    If auto is selected, the type will be determined by the presence of TCRData or BCRData columns in the metadata. If both columns are present, TCR will be selected by default.
    
• combineTCR (type=json): Default: {'samples': True}.
  The extra arguments for scRepertoire::combineTCR function.
  See also https://www.borch.dev/uploads/screpertoire/reference/combinetcr
• combineBCR (type=json): Default: {'samples': True}.
  The extra arguments for scRepertoire::combineBCR function.
  See also https://www.borch.dev/uploads/screpertoire/reference/combinebcr
• exclude (auto): Default: ['BCRData', 'TCRData', 'RNAData'].
  The columns to exclude from the metadata to add to the object.
  A list of column names to exclude or a string with column names separated by ,. By default, BCRData, TCRData and RNAData will be excluded.
  
• tmpdir: Default: /tmp.
  The temporary directory to store the symbolic links to the TCR/BCR data files.
  
• format (choice): The format of the TCR/BCR data files.
  
  • 10X: 10X Genomics data, which is usually in a directory with filtered_contig_annotations.csv file.
    
  • AIRR: AIRR format, which is usually in a file with airr_rearrangement.tsv file.
    
  • BD: Becton Dickinson data, which is usually in a file with Contigs_AIRR.tsv file.
    
  • Dandelion: Dandelion data, which is usually in a file with all_contig_dandelion.tsv file.
    
  • Immcantation: Immcantation data, which is usually in a file with data.tsv file.
    
  • JSON: JSON format, which is usually in a file with .json extension.
    
  • ParseBio: ParseBio data, which is usually in a file with barcode_report.tsv file.
    
  • MiXCR: MiXCR data, which is usually in a file with clones.tsv file.
    
  • Omniscope: Omniscope data, which is usually in a file with .csv extension.
    
  • TRUST4: TRUST4 data, which is usually in a file with barcode_report.tsv file.
    
  • WAT3R: WAT3R data, which is usually in a file with barcode_results.csv file.
    See also: https://rdrr.io/github/ncborcherding/scRepertoire/man/loadContigs.html If not provided, the format will be guessed from the file name by scRepertoire::loadContigs().