MuSiC does the signature creation in one step, not separated into build_model and deconvolute. Please use the deconvolute method with your single cell and bulk RNA seq data to use MuSiC.
build_model_music(
single_cell_object,
cell_type_annotations,
batch_ids,
non_zero = TRUE,
markers = NULL,
clusters = "cellType",
samples = "batchId",
select_ct = NULL,
cell_size = NULL,
ct_cov = FALSE,
verbose = FALSE
)A matrix with the single-cell data. Rows are genes, columns are samples. Row and column names need to be set.
A vector of the cell type annotations. Has to be in the same order as the samples in single_cell_object.
A vector of the ids of the samples or individuals.
logical, default as TRUE. If true, remove all gene with zero expression.
vector or list of gene names, default as NULL. If NULL, use all genes.
character, the name of the phenoData of the single cell dataset used as clusters.
character, the name of the phenoData of the single cell dataset used as samples.
vector of cell types. Default as NULL. If NULL, then use all cell types provided.
data.frame of cell sizes. 1st column contains the names of cell types, 2nd column has the cell sizes per cell type. Default as NULL. If NULL, then estimate cell size from data.
logical. If TRUE, use the covariance across cell types.
Whether to produce an output on the console.
a list with elements:
gene by cell type matrix of Design matrix
subject by celltype matrix of Library size
vector of average library size for each cell type
gene by celltype matrix of average relative abundance
gene by celltype matrix of cross-subject variation