Deconvolute with CIBERSORTx

Deconvolute with CIBERSORTx

deconvolute_cibersortx(
  bulk_gene_expression,
  signature,
  single_cell_object = NULL,
  cell_type_annotations = NULL,
  rmbatch_B_mode = FALSE,
  rmbatch_S_mode = FALSE,
  verbose = FALSE,
  container = c("docker", "apptainer"),
  container_path = NULL,
  input_dir = NULL,
  output_dir = NULL,
  display_extra_info = FALSE,
  label = "none",
  ...
)

Arguments

bulk_gene_expression

A matrix or dataframe with the bulk data. Rows are genes, columns are samples. Row and column names need to be set. Can also just be the filename of the bulk expression data in the correct format (generated by using this method). The file needs to be in the folder "input_dir".

signature

The signature matrix. Can also be the filename of the signature matrix in the correct format (generated by using this method). The file needs to be in the folder "input_dir".

single_cell_object

A matrix with the single-cell data. Rows are genes, columns are samples. Row and column names need to be set. (optional, only necessary if S- or B-mode are used)

cell_type_annotations

A vector of the cell type annotations. Has to be in the same order as the samples in single_cell_object. (optional, only necessary if S- or B-mode are used)

rmbatch_B_mode

Run B-mode batch correction (default: FALSE). Supply single_cell_object if TRUE.

rmbatch_S_mode

Run S-mode batch correction (default: FALSE). Supply single_cell_object if TRUE.

verbose

Whether to produce an output on the console.

container

The container used to run the method. The possibilities are 'docker' (default) or 'apptainer'

container_path

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

input_dir

The folder 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_extra_info

Whether to print the "P.value","Correlation" and "RMSE" calculated by CIBERSORTx.

label

The label which will be added to the file name. Default is "none", adding no label at all.

...

Additional parameters supplied to the algorithm. Options are:

• perm No. of permutations for p-value calculation (default: 0).

• source_GEPs <file_name> Signature matrix GEPs for batch correction (default: sigmatrix).

• qn Run quantile normalization (default: FALSE).

• absolute Run absolute mode (default: FALSE).

• abs_method Pick absolute method ("sig.score" (default) or "no.sumto1").

Value

A matrix with the probabilities of each cell-type for each individual. Rows are individuals, columns are cell types.