getSHM calculates somatic hypermutation (i.e. 1 - (percentage identity to germline VH gene)).
Usage
getSHM(SeuratObj, v_identity_anno_name, shm_column_to_add = "shm")
Arguments
- SeuratObj
Seurat Object
- v_identity_anno_name
column name in the Seurat meta.data slot which holds the v_identity information to be considered.
- shm_column_to_add
name of column to be added to the Seurat meta.data slot
which holds the SHM frequency calculated in this function
Value
The same Seurat object as given by SeuratObj, except that a new column with
name given by shm_column_to_add is appended to the SeuratObj meta.data slot to reflects
the calculated SHM frequency.
Details
getSHM considers the v_identity (i.e.
mapped to each cell, and calculate 1 - v_identity as the somatic hypermutation (SHM)
level for the cell. It finds the v_identity information from the meta.data slot of the Seurat object.
For cells without a mapped V sequence, it will impute SHM as 0.