xCellAnalysis: The xCell Analysis Pipeline

In IOBR: Immune Oncology Biological Research

The xCell Analysis Pipeline

Description

Returns the xCell cell types enrichment scores for tumor microenvironment deconvolution. Uses ssGSEA-based enrichment analysis with spillover compensation to estimate cell type proportions from gene expression data.

Usage

xCellAnalysis(
  expr,
  signatures = NULL,
  genes = NULL,
  spill = NULL,
  rnaseq = TRUE,
  file.name = NULL,
  scale = TRUE,
  alpha = 0.5,
  save.raw = FALSE,
  cell.types.use = NULL
)

Arguments

expr	Gene expression data matrix with row names as gene symbols and columns as samples.
signatures	GMT object of signatures. If 'NULL', uses xCell defaults.
genes	Character vector of genes to use in the analysis. If 'NULL', uses xCell defaults.
spill	Spillover object for adjusting scores. If 'NULL', uses xCell defaults.
rnaseq	Logical indicating whether to use RNA-seq (TRUE) or array (FALSE) spillover parameters. Default is 'TRUE'.
file.name	Character string for saving scores. Default is 'NULL'.
scale	Logical indicating whether to use scaling. Default is 'TRUE'.
alpha	Numeric value to override spillover alpha parameter. Default is '0.5'.
save.raw	Logical indicating whether to save raw scores. Default is 'FALSE'.
cell.types.use	Character vector of cell types to use. If 'NULL', uses all available cell types. Default is 'NULL'.

Value

A matrix of adjusted xCell scores.

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