xCellAnalysis: The xCell analysis pipeline

In IOBR/IOBR: Immune Oncology Biological Research

The xCell analysis pipeline

Description

The xCell analysis pipeline

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	the gene expression data set. A matrix with row names as symbols and columns as samples.
signatures	a GMT object of signatures.
genes	list of genes to use in the analysis.
spill	the Spillover object for adjusting the scores.
rnaseq	if true than use RNAseq spillover and calibration paramters, else use array parameters.
file.name	string for the file name for saving the scores. Default is NULL.
scale	if TRUE, uses scaling to trnasform scores using fit.vals
alpha	a value to override the spillover alpha parameter. Deafult = 0.5
save.raw	TRUE to save a raw
cell.types.use	a character list of the cell types to use in the analysis. If NULL runs xCell with all cell types. The spillover compensation step may over compensate, thus it is always better to run xCell with a list of cell types that are expected to be in the mixture. The names of cell types in this list must be a subset of the cell types that are inferred by xCell.

Value

the adjusted xCell scores

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.