align_sers: Aligns a list of ser objects

In Chris-Cherry/sctools: Single cell analysis tools package

Description

This function integrates separate batches of cells typically processed by process_counts_hash.

Usage

align_sers(sers, meta_file = "metadata.csv", ref = NULL)

Arguments

sers	A list of Seurat objects to align. The objects should be normalized with variable genes ID'd.
meta_file	Path to a metadata file containing all metadata by sample. Cell barcodes should be sample_name-XXXXXXXX and the metadata file should have sample_name as the first column.
ref	NULL or integer specifying which ser in the sers list to use as a reference. If NULL then all combinations will be calculated and the best integration pass selected.

Value

Integrated Seurat object with mnn components as pca reduction.

Chris-Cherry/sctools documentation built on Jan. 25, 2022, 2:19 p.m.