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TME Deconvolution Methods

Source: R/deconvo_tme.R
tme_deconvolution_methods.Rd

A named vector of supported tumor microenvironment (TME) deconvolution methods in the IOBR package.

Usage

tme_deconvolution_methods

Format

A named character vector where names are display names and values are internal method names.

Value

Named character vector of available deconvolution methods.

Details

The methods currently supported are:

  • `mcpcounter`: MCP-counter for immune and stromal cell populations

  • `epic`: EPIC for immune, stromal, and cancer cell fractions

  • `xcell`: xCell for 64 immune and stromal cell types

  • `cibersort`: CIBERSORT for 22 immune cell types

  • `cibersort_abs`: CIBERSORT in absolute mode

  • `ips`: Immunophenoscore calculation

  • `estimate`: ESTIMATE for stromal/immune/estimate scores

  • `svr`: Support Vector Regression (custom reference)

  • `lsei`: Least Squares with Equality/Inequality constraints

  • `timer`: TIMER for cancer-specific immune estimation

  • `quantiseq`: quanTIseq for RNA-seq immune deconvolution

Examples

# List all available TME deconvolution methods
tme_deconvolution_methods
#>         MCPcounter               EPIC              xCell          CIBERSORT 
#>       "mcpcounter"             "epic"            "xcell"        "cibersort" 
#> CIBERSORT Absolute                IPS           ESTIMATE                SVR 
#>    "cibersort_abs"              "ips"         "estimate"              "svr" 
#>               lsei              TIMER          quanTIseq 
#>             "lsei"            "timer"        "quantiseq" 

# Get internal method name for a specific method
tme_deconvolution_methods["MCPcounter"]
#>   MCPcounter 
#> "mcpcounter"