reference_map: Compare a query scRNA-seq dataset with a reference

In quadbiolab/VoxHunt: Projecting single-cell transcriptomes to spatial brain maps

Compare a query scRNA-seq dataset with a reference

Description

Calculates correlation between single-cell gene expression.

Usage

reference_map(object, ...)

## Default S3 method:
reference_map(
  object,
  reference_object,
  query_meta = NULL,
  reference_meta = NULL,
  groups = NULL,
  reduction = NULL,
  method = "pearson",
  genes_use = NULL,
  allow_neg = FALSE,
  pseudobulk_groups = TRUE
)

## S3 method for class 'Seurat'
reference_map(
  object,
  reference_object,
  slot = "data",
  assay = "RNA",
  group_name = NULL,
  reduction = "umap",
  method = "pearson",
  genes_use = NULL,
  allow_neg = FALSE,
  pseudobulk_groups = TRUE
)

Arguments

object	A matrix with query expression data.
reference_object	A matrix with reference expression data.
reference_meta	A data frame with reference metadata.
groups	A character or factor vector or for grouping of cells, e.g. clusters, cell types.
method	A character string indicating which correlation coefficient to compute.
genes_use	A character vector with genes to use for computing the correlation. We recommend to use 150 - 500 genes.
allow_neg	Logical. Whether to allow negative correlations or set them to 0.
pseudobulk_groups	Logical. Whether to summarize the group expression before computing the correlation.
group_name	A string indicating the metadata column for grouping the cells, e.g. clusters, cell types.

Value

A ReferenceMap object with a cell x cell correlation matrix and metadata.

quadbiolab/VoxHunt documentation built on March 4, 2024, 6:37 a.m.