deconvo_cibersort: Decoding immune microenvironment using CIBERSORT
In IOBR/IOBR: Immune Oncology Biological Research

deconvo_cibersort

R Documentation

Decoding immune microenvironment using CIBERSORT

Description

CIBERSORT is only freely available to academic users. A license an the binary can be obtained from https://cibersort.stanford.edu.

Usage

deconvo_cibersort(
  eset,
  project = NULL,
  arrays,
  perm = 1000,
  absolute = FALSE,
  abs_method = "sig.score"
)

Arguments

`eset`	expression set with gene symbol at row name, sample ID at column
`project`	project name used to distinguish different data sets
`arrays`	logical: Runs methods in a mode optimized for microarray data.
`perm`	permutation to run CIBERSORT
`absolute`	logical: Runs CIBERSORT in absolute mode

Value

cibersrot with immune cell fractions

Author(s)

Dongqiang Zeng

Examples

# Loading TCGA-STAD expresion data(raw count matrix)
data(eset_stad, package = "IOBR")
eset <- count2tpm(countMat = eset_stad, source = "local", idType = "ensembl")
cibersort_result<-deconvo_cibersort(eset = eset,project = "TCGA-STAD", arrays = FALSE, absolute = FALSE, perm = 500)

IOBR/IOBR documentation built on April 4, 2024, 1:07 a.m.