Deconvolution with default methods

library(multideconv)

The basic function is to perform cell type deconvolution using six default methods (quanTIseq, DeconRNASeq, CIBERSORTx, EpiDISH, DWLS, MOMF) and nine default signatures (see paper Hurtado et al., 2025). The function accepts either raw counts or TPM-normalized counts as input (with genes as SYMBOL).

NOTE: If you plan to use CIBERSORTx, you must provide your credentials (see README for details). The resulting deconvolution matrix is automatically saved in the Results/ directory.

The output includes all combinations of deconvolution features, method-signature-cell type.

bulk = multideconv::raw_counts
deconv = compute.deconvolution(raw.counts = bulk, 
                               methods = c("Quantiseq", "Epidish", 
                                           "DeconRNASeq", "DWLS","MOMF"), 
                               normalized = TRUE, 
                               return = TRUE, 
                               file_name = "Tutorial")

To exclude specific methods or signatures, use the methods or signatures_exclude arguments:

deconv = compute.deconvolution(raw.counts = bulk, 
                               methods = c("Quantiseq", "DeconRNASeq"), 
                               normalized = TRUE,
                               signatures_exclude = "BPRNACan", 
                               return = TRUE, 
                               file_name = "Tutorial")

To speed up computation, multideconv supports parallelization. Set doParallel = TRUE and specify the number of workers based on your system’s resources:

deconv = compute.deconvolution(raw.counts = bulk, 
                               methods = "DWLS", 
                               normalized = TRUE, 
                               return = TRUE, 
                               file_name = "Tutorial", 
                               doParallel = TRUE, 
                               workers = 3)

Cell type signatures

In order to access the default signatures multideconv provides, you can do the following:

To list all signatures

path <- system.file("signatures/", package = "multideconv")
list.files(path)
#>  [1] "BPRNACan.txt"                  "BPRNACan3DProMet.txt"         
#>  [3] "BPRNACanProMet.txt"            "CBSX-HNSCC-scRNAseq.txt"      
#>  [5] "CBSX-Melanoma-scRNAseq.txt"    "CBSX-NSCLC-PBMCs-scRNAseq.txt"
#>  [7] "CBSX-NSCLC-scRNAseq.txt"       "CCLE-TIL10.txt"               
#>  [9] "LM22.txt"                      "MCPcounter"                   
#> [11] "TIL10.txt"

To access a specific signature

signature = read.delim(paste0(path, "CBSX-Melanoma-scRNAseq.txt"))
head(signature)
#>     NAME Malignant Endothelial.cells      CAF T.cells.CD8 NK.cells Macrophages
#> 1    A2M 272.91408         212.14093  1.00000     1.00000   1.0000    700.2033
#> 2 A4GALT   1.00000          67.08075  1.00000     1.00000   1.0000      1.0000
#> 3  ABCA1   1.00000          84.22255  1.00000     1.00000   1.0000    128.7594
#> 4  ABCB1   1.00000           1.00000  1.00000     1.00000 133.5748      1.0000
#> 5  ABCB5 117.86677           1.00000  1.00000    19.94351   1.0000      1.0000
#> 6  ABCB6  49.62804           1.00000 41.38285     1.00000   1.0000      1.0000
#>   T.cells.CD4 B.cells
#> 1           1       1
#> 2           1       1
#> 3           1       1
#> 4           1       1
#> 5           1       1
#> 6           1       1