build_model_cibersortx: Signature matrix creation with CIBERSORTx

In PelzKo/immunedeconv2: Second generation methods for immune cell deconvolution

Signature matrix creation with CIBERSORTx

Description

Signature matrix creation with CIBERSORTx

Usage

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.

PelzKo/immunedeconv2 documentation built on Feb. 12, 2025, 4:16 p.m.