CDR3AAPhyschem

CDR3 AA physicochemical feature analysis

The idea is to perform a regression between two groups of cells (e.g. Treg vs Tconv) at different length of CDR3 AA sequences.
The regression will be performed for each physicochemical feature of the AA (hydrophobicity, volume and isolectric point).

Environment Variables

  • group: The key of group in metadata to define the groups to compare. For example, CellType, which has cell types annotated for each cell in the combined object (immdata + Seurat metadata)
  • comparison (type=json): A dict of two groups, with keys as the group names and values as the group labels. For example, 
    Treg = ["CD4 CTL", "CD4 Naive", "CD4 TCM", "CD4 TEM"]
Tconv = "Tconv"
  • prefix: Default: {Sample}_.
    The prefix of the cell names (rownames) in the metadata.
    The prefix is usually not needed in immdata, as the data is stored in the immdata object separately for each sample. However, the Seurat object has a combined meta.data for all the samples, so the prefix is needed. Usually, the prefix is the sample name.
    For example, Sample1-AACGTTGAGGCTACGT-1.
    We need this prefix to add the sample name to the cell names in immdata, so that we can match the cells in immdata and Seurat object. Set it to None or an empty string if the Seurat object has the same cell names as immdata. You can use placeholders to specify the prefix, e.g., {Sample}_. In such a case, the Sample column must exist in the Seurat object.
  • target: Which group to use as the target group. The target group will be labeled as 1, and the other group will be labeled as 0 in the regression.
  • subset: A column, or a list of columns separated by comma, in the merged object to subset the cells to perform the regression, for each group in the columns.
    If not provided, all the cells will be used.

Reference