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Deconvolute using CIBERSORTx Docker image

Source: R/deconvolute_cibersortx.R
deconvolute_cibersortx.Rd

Performs deconvolution of bulk proteome data into constituent cell types using the CIBERSORTx Docker image. This function handles the interaction with the Docker container and processes the results.

Usage

deconvolute_cibersortx(
  data,
  signature,
  perm = 1,
  rmbatch_S_mode = FALSE,
  source_GEPs = NULL,
  rmbatch_B_mode = FALSE,
  QN = FALSE,
  absolute = FALSE,
  abs_method = "sig.score",
  use_sudo = FALSE
)

Arguments

data

A numeric matrix containing mixture data with genes as row names and samples as columns.

signature

A numeric matrix containing the signature matrix with genes as row names and cell types as columns.

perm

An integer specifying the number of permutations to be performed. Default is 1.

rmbatch_S_mode

A logical value indicating whether to remove batch effects in source GEPs mode. Default is FALSE.

source_GEPs

A matrix containing the source gene expression profiles. Required if rmbatch_S_mode is TRUE.

rmbatch_B_mode

A logical value indicating whether to remove batch effects in bulk mode. Default is FALSE.

QN

A logical value indicating whether to perform quantile normalization. Default is FALSE.

absolute

A logical value indicating whether to use absolute mode. Default is FALSE.

abs_method

A character string specifying the method to use for absolute mode. Default is "sig.score".

use_sudo

A logical value indicating whether to use sudo for Docker commands. Default is FALSE.

Value

A numeric matrix with samples as rows and cell types as columns, representing the estimated proportion of each cell type in each sample.

Details

This function requires the CIBERSORTx Docker image to be installed and the CIBERSORTX_EMAIL and CIBERSORTX_TOKEN environment variables to be set. You can get these credentials by registering at the CIBERSORTx website (https://cibersortx.stanford.edu/).

The function creates temporary files for the mixture data and signature matrix, runs the CIBERSORTx Docker container, and processes the results. Note that absolute mode is not currently supported in the Docker version.

See also

deconvolute_cibersort for using the R implementation of CIBERSORT, deconvolute for a unified interface to multiple deconvolution methods.

Examples

if (FALSE) { # \dontrun{
# Set required environment variables (ideally in .Renviron)
Sys.setenv(CIBERSORTX_EMAIL = "your.email@example.com")
Sys.setenv(CIBERSORTX_TOKEN = "your-token-here")

# Load example data and signature matrix
data_file <- system.file("extdata", "mixed_samples_matrix.rds", package = "proteoDeconv")
mixed_samples <- readRDS(data_file)

signature_file <- system.file("extdata", "cd8t_mono_signature_matrix.rds", package = "proteoDeconv")
signature_matrix <- readRDS(signature_file)

# Run deconvolution with CIBERSORTx Docker
result <- deconvolute_cibersortx(
  data = mixed_samples,
  signature = signature_matrix,
  perm = 100,
  QN = TRUE
)
} # }