ImmunarchLoading¶

Immuarch - Loading data

Load the raw data into immunarch object, using immunarch::repLoad().

For the data path specified at TCRData in the input file, we will first find filtered_contig_annotations.csv and filtered_config_annotations.csv.gz in the path. If neighter of them exists, we will find all_contig_annotations.csv and all_contig_annotations.csv.gz in the path and a warning will be raised (You can find it at ./.pipen/<pipeline-name>/ImmunarchLoading/0/job.stderr).

If none of the files exists, an error will be raised.

This process will also generate a text file with the information for each cell.
The file will be saved at ./.pipen/<pipeline-name>/ImmunarchLoading/0/output/<prefix>.tcr.txt.
The file can be used by the IntegratingTCR process to integrate the TCR-seq data into the Seurat object for further integrative analysis.
envs.metacols can be used to specify the columns to be exported to the text file.

Input¶

• metafile: The meta data of the samples A tab-delimited file Two columns are required:
  
  • Sample to specify the sample names.
    
  • TCRData to assign the path of the data to the samples, and this column will be excluded as metadata.
    Immunarch is able to fetch the sample names from the names of the target files. However, 10x data yields result like filtered_contig_annotations.csv, which doesn't have any name information.
    

Output¶

• rdsfile: Default: {{in.metafile | stem}}.immunarch.RDS.
  The RDS file with the data and metadata
• metatxt: Default: {{in.metafile | stem}}.tcr.txt.
  The meta data at cell level, which can be used to attach to the Seurat object

Environment Variables¶

• prefix: Default: {Sample}_.
  The prefix to the barcodes. You can use placeholder like {Sample}_ to use the meta data from the immunarch object. The prefixed barcodes will be saved in out.metatxt. The immunarch object keeps the original barcodes, but the prefix is saved at immdata$prefix.
  

  Note

  This option is useful because the barcodes for the cells from scRNA-seq data are usually prefixed with the sample name, for example, Sample1_AAACCTGAGAAGGCTA-1. However, the barcodes for the cells from scTCR-seq data are usually not prefixed with the sample name, for example, AAACCTGAGAAGGCTA-1. So we need to add the prefix to the barcodes for the scTCR-seq data, and it is easier for us to integrate the data from different sources later.
  

• tmpdir: Default: /tmp.
  The temporary directory to link all data files.
  Immunarch scans a directory to find the data files. If the data files are not in the same directory, we can link them to a temporary directory and pass the temporary directory to Immunarch.
  This option is useful when the data files are in different directories.
  

• mode: Default: paired.
  Either "single" for single chain data or "paired" for paired chain data. For single, only TRB chain will be kept at immdata$data, information for other chains will be saved at immdata$tra and immdata$multi.
  
• extracols (list): Default: [].
  The extra columns to be exported to the text file.
  You can refer to the immunarch documentation to get a sense for the full list of the columns.
  The columns may vary depending on the data source.
  The columns from immdata$meta and some core columns, including Barcode, CDR3.aa, Clones, Proportion, V.name, J.name, and D.name will be exported by default. You can use this option to specify the extra columns to be exported.