build_atlas {clustifyr} | R Documentation

## 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)

[Package clustifyr version 1.4.0 Index]