build_atlas: Function to combine records into single atlas

View source: R/utils.R

build_atlasR Documentation

Function to combine records into single atlas


Function to combine records into single atlas


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



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)


text file with a single column containing genes and the ordering desired in the output matrix


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 filename for .rds file. If NULL the matrix will be returned instead of saving


Combined matrix with all genes given


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/RClusterCT documentation built on July 10, 2022, 6:18 a.m.