expression2List: _*DEPRECATED*_ Take the meta data in seurat/SCE and place it...

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

DEPRECATED Take the meta data in seurat/SCE and place it into a list

Description

Allows users to perform more fundamental measures of clonotype analysis using the meta data from the seurat or SCE object. For Seurat objects the active identity is automatically added as "cluster". Remaining grouping parameters or SCE or Seurat objects must appear in the meta data.

This function is deprecated as of version 2 due to the confusion it caused to many users. Users are encouraged to remain with the abstraction barrier of combined single cell objects and the outputs of combineTCR() and combineBCR() for all functions.

We discourage the use of this function, but if you have to use it, set the force argument to TRUE.

Usage

expression2List(sc, ..., force = FALSE)

Arguments

sc	output of combineExpression().
...	previously the group or split.by argument, indicating the column header to group the new list by. This should strictly be one argument and is an ellipsis for backwards compatibility. Everything after the first argument is ignored.
force	logical. If not TRUE (default), a deprecation error will be thrown. Otherwise the function will run but not guaranteed to be stable.

Value

list derived from the meta data of single-cell object with elements divided by the group parameter

ncborcherding/scRepertoire documentation built on Jan. 30, 2025, 5:07 p.m.