deconvo_ref: Deconvolve Using Custom Reference

In IOBR: Immune Oncology Biological Research

Deconvolve Using Custom Reference

Description

Cell fraction estimation using SVR or lsei methods with custom reference.

Usage

deconvo_ref(
  eset,
  project = NULL,
  arrays = TRUE,
  method = c("svr", "lsei"),
  perm = 100,
  reference,
  scale_reference = TRUE,
  absolute.mode = FALSE,
  abs.method = "sig.score"
)

Arguments

eset	Gene expression matrix.
project	Optional project name. Default is 'NULL'.
arrays	Logical: use quantile normalization. Default is 'TRUE'.
method	Method: '"svr"' or '"lsei"'. Default is '"svr"'.
perm	Permutations for SVR. Default is 100.
reference	Custom reference matrix (e.g., lm22, lm6).
scale_reference	Logical: scale reference. Default is 'TRUE'.
absolute.mode	Logical: absolute mode for SVR. Default is 'FALSE'.
abs.method	Method for absolute mode. Default is '"sig.score"'.

Value

Data frame with cell fractions. Columns suffixed with '_CIBERSORT'.

Author(s)

Dongqiang Zeng, Rongfang Shen

Examples

# Simulate data
set.seed(123)
sim_ref <- matrix(rnorm(100 * 5), 100, 5)
rownames(sim_ref) <- paste0("Gene", 1:100)
colnames(sim_ref) <- paste0("CellType", 1:5)

sim_eset <- matrix(rnorm(100 * 3), 100, 3)
rownames(sim_eset) <- paste0("Gene", 1:100)
colnames(sim_eset) <- paste0("Sample", 1:3)

# Run deconvolution
result <- deconvo_ref(eset = sim_eset, reference = sim_ref, method = "lsei")
if (!is.null(result)) head(result)

IOBR documentation built on May 30, 2026, 5:07 p.m.