Signature matrix creation with CIBERSORTx

build_model_cibersortx(
  single_cell_object,
  cell_type_annotations,
  container = c("docker", "apptainer"),
  container_path = NULL,
  verbose = FALSE,
  input_dir = NULL,
  output_dir = NULL,
  display_heatmap = FALSE,
  k_max = 999,
  ...
)

Arguments

single_cell_object

A matrix with the single-cell data. Rows are genes, columns are samples. Row and column names need to be set.

cell_type_annotations

A vector of the cell type annotations. Has to be in the same order as the samples in single_cell_object.

container

The container used ot run the method. The possibilities are 'docker' (default) or 'apptainer'. You can check if the container can be called with the check_container() function

container_path

the path where the apptainer .sif file is/will be stored (optional)

verbose

Whether to produce an output on the console.

input_dir

The directory in which the input files can be found (or are created in). Default is a temporary directory.

output_dir

The directory in which the output files are saved. Default is a temporary directory.

display_heatmap

Whether to display the generated heatmap.

k_max

Maximum condition number (default: 999). Will be added to the file name.

...

Additional parameters supplied to the algorithm. Options are:

g_min Minimum number of genes per cell type in sig. matrix (default: 300).
g_max Maximum number of genes per cell type in sig. matrix (default: 500).
q_value Q-value threshold for differential expression (default: 0.01).
filter Remove non-hematopoietic genes (default: FALSE).
remake Remake signature gene matrix (default: False).
replicates Number of replicates to use for building scRNAseq reference file (default: 5).
sampling Fraction of available single cell GEPs selected using random sampling (default: 0.5).
fraction Fraction of cells of same identity showing evidence of expression (default: 0.75).

Value

The signature matrix. Rows are genes, columns are cell types.