Deconvolute with CIBERSORTx
deconvolute_cibersortx(
bulk_gene_expression,
signature,
verbose = FALSE,
container = c("docker", "singularity"),
container_path = NULL,
input_dir = NULL,
output_dir = NULL,
display_extra_info = FALSE,
label = "none",
...
)
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".
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".
Whether to produce an output on the console.
The container used to run the method. The possibilities are 'docker' (default) or 'singularity'
the path where the singularity .sif file is/will be stored (optional)
The folder in which the input files can be found (or are created in). Default is a temporary directory.
The directory in which the output files are saved. Default is a temporary directory.
Whether to print the "P.value","Correlation" and "RMSE" calculated by CIBERSORTx.
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
rmbatch_B_mode
rmbatch_S_mode
source_GEPs <file_name> Signature matrix GEPs for batch correction (default: sigmatrix).
qn
absolute
abs_method
A matrix with the probabilities of each cell-type for each individual. Rows are individuals, columns are cell types.