ScRepCombiningExpression

Combine the scTCR/BCR data with the expression data

This process combines the scTCR/BCR data with the expression data using scRepertoire::combineExpression function. The expression data should be in Seurat format. The scRepertoire object should be a combined contig object, usually generated by scRepertoire::combineTCR or scRepertoire::combineBCR.

See also: https://www.borch.dev/uploads/screpertoire/reference/combineexpression.

Input

  • screpfile: The scRepertoire object in RDS/qs format
  • srtobj: The Seurat object, saved in RDS/qs format

Output

  • outfile: Default: {{in.screpfile | stem}}.qs.
    The Seurat object with the TCR/BCR data combined In addition to the meta columns added by scRepertoire::combineExpression(), a new column VDJ_Presence will be added to the metadata. It indicates whether the cell has a TCR/BCR sequence or not. The value is TRUE if the cell has a TCR/BCR sequence, and FALSE otherwise.

Environment Variables

  • cloneCall: Default: aa.
    How to call the clone - VDJC gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), VDJC gene + CDR3 nucleotide (strict) or a custom variable in the data.
  • chain: Default: both.
    indicate if both or a specific chain should be used e.g. "both", "TRA", "TRG", "IGH", "IGL".
  • group_by: Default: Sample.
    The column label in the combined clones in which clone frequency will be calculated. NULL or "none" will keep the format of input.data.
  • proportion (flag): Default: True.
    Whether to proportion (TRUE) or total frequency (FALSE) of the clone based on the group_by variable.
  • filterNA (flag): Default: False.
    Method to subset Seurat/SCE object of barcodes without clone information
  • cloneSize (type=json): Default: {'Rare': 0.0001, 'Small': 0.001, 'Medium': 0.01, 'Large': 0.1, 'Hyperexpanded': 1}.
    The bins for the grouping based on proportion or frequency.
    If proportion is FALSE and the cloneSizes are not set high enough based on frequency, the upper limit of cloneSizes will be automatically updated.
  • addLabel (flag): Default: False.
    This will add a label to the frequency header, allowing the user to try multiple group_by variables or recalculate frequencies after subsetting the data.