SplitSeurat: Split Seurat

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

Split Seurat

Description

Split a seurat object, dividing into new objects based on the value of a field

Usage

SplitSeurat(
  seuratObj,
  splitField,
  minCellsToKeep = 0.02,
  naOtherLabel = "Other",
  excludedClasses = NULL,
  appendLowFreqToOther = TRUE,
  alwaysRetainOtherClass = FALSE
)

Arguments

seuratObj	The seurat object
splitField	The name of the field on which to split the object
minCellsToKeep	If any of the resulting seurat objects have less than this many cells, they will be discarded. If this value is less than 1, it will be interpreted as a fraction of the total input cells.
naOtherLabel	This string will be used to label any cells marked NA.
excludedClasses	Any cells with these labels will be lumped into the NA/Other bin.
appendLowFreqToOther	If true, any cells with NAs for the splitField, or terms with fewer than minCellsToKeep, will be merged into a single seurat object
alwaysRetainOtherClass	If true, even if the number of cells is less than minCellsToKeep, this class with be retained.

bimberlabinternal/CellMembrane documentation built on Oct. 16, 2024, 6:53 a.m.