merge.Seurat: Merge Seurat Objects

In lambdamoses/SeuratBasics: Slimmed down version of Seurat

Description

Merge two or more objects.

Usage

## S3 method for class 'Assay'
merge(x = NULL, y = NULL, add.cell.ids = NULL, merge.data = TRUE, ...)

## S3 method for class 'Seurat'
merge(
  x = NULL,
  y = NULL,
  add.cell.ids = NULL,
  merge.data = TRUE,
  project = "SeuratProject",
  ...
)

Arguments

x	Object
y	Object (or a list of multiple objects)
add.cell.ids	A character vector of length(x = c(x, y)). Appends the corresponding values to the start of each objects' cell names.
merge.data	Merge the data slots instead of just merging the counts (which requires renormalization). This is recommended if the same normalization approach was applied to all objects.
...	Arguments passed to other methods
project	Sets the project name for the Seurat object.

Details

When merging Seurat objects, the merge procedure will merge the Assay level counts and potentially the data slots (depending on the merge.data parameter). It will also merge the cell-level meta data that was stored with each object and preserve the cell identities that were active in the objects pre-merge. The merge will not preserve reductions, graphs, logged commands, or feature-level metadata that were present in the original objects. If add.cell.ids isn't specified and any cell names are duplicated, cell names will be appended with _X, where X is the numeric index of the object in c(x, y).

Value

Merged object

Examples

# merge two objects
merge(x = pbmc_small, y = pbmc_small)
# to merge more than two objects, pass one to x and a list of objects to y
merge(x = pbmc_small, y = c(pbmc_small, pbmc_small))

lambdamoses/SeuratBasics documentation built on May 6, 2020, 9:32 a.m.