build_atlas: Function to combine records into single atlas

In NCBI-Hackathons/clustifyR: Classifier for Single-cell RNA-seq Using Cell Clusters

Function to combine records into single atlas

Description

Function to combine records into single atlas

Usage

build_atlas(matrix_fns = NULL, genes_fn, matrix_objs = NULL, output_fn = NULL)

Arguments

matrix_fns	character vector of paths to study matrices stored as .rds files. If a named character vector, then the name will be added as a suffix to the cell type name in the final matrix. If it is not named, then the filename will be used (without .rds)
genes_fn	text file with a single column containing genes and the ordering desired in the output matrix
matrix_objs	Checks to see whether .rds files will be read or R objects in a local environment. A list of environmental objects can be passed to matrx_objs, and that names will be used, otherwise defaults to numbers
output_fn	output filename for .rds file. If NULL the matrix will be returned instead of saving

Value

Combined matrix with all genes given

Examples

pbmc_ref_matrix <- average_clusters(
    mat = pbmc_matrix_small,
    metadata = pbmc_meta,
    cluster_col = "classified",
    if_log = TRUE # whether the expression matrix is already log transformed
)
references_to_combine <- list(pbmc_ref_matrix, cbmc_ref)
atlas <- build_atlas(NULL, human_genes_10x, references_to_combine, NULL)

NCBI-Hackathons/clustifyR documentation built on Aug. 31, 2024, 5:35 a.m.