Compute deconvolution methods with variable signatures

Usage

compute_methods_variable_signature(
  TPM_matrix,
  signatures,
  algos = c("CBSX", "Epidish", "DeconRNASeq", "DWLS", "MOMF"),
  exclude = NULL,
  cbsx.name,
  cbsx.token,
  doParallel = FALSE,
  workers = NULL,
  sc_obj = NULL
)

Arguments

TPM_matrix: A matrix with TPM normalized counts (samples as columns and genes symbols as rows)
signatures: A path with a directory where signatures are located
algos: A character vector with the methods to compute (Default methods are CBSX, Epidish, DeconRNASeq and DWLS)
exclude: (Optional) A character vector with the signature to exclude
cbsx.name: CIBERSORTx credential mail if CBSX will be run
cbsx.token: CIBERSORTx credential token if CBSX will be run
doParallel: Boolean value to specify if DWLS and CBSX should run in parallel (default is False)
workers: Number of worker process to run during parallelization (default is NULL)
sc_obj: A matrix with the counts from scRNAseq object (genes as rows and cells as columns) to run MOMF method. If NULL, MOMF is ignored.

Value

A matrix with the deconvolution features corresponding to all combinations of methods-signatures specified

References

Sturm, G., Finotello, F., Petitprez, F., Zhang, J. D., Baumbach, J., Fridman, W. H., ..., List, M., Aneichyk, T. (2019). Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. Bioinformatics, 35(14), i436-i445. https://doi.org/10.1093/bioinformatics/btz363

Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data. Dietrich, Alexander and Merotto, Lorenzo and Pelz, Konstantin and Eder, Bernhard and Zackl, Constantin and Reinisch, Katharina and Edenhofer, Frank and Marini, Federico and Sturm, Gregor and List, Markus and Finotello, Francesca. (2024) https://doi.org/10.1101/2024.06.10.598226