deconvo_ref: Estimate the fraction of cell types using defined reference...

View source: R/deconvo_tme.R

deconvo_refR Documentation

Estimate the fraction of cell types using defined reference genes

Description

Estimate the fraction of cell types using defined reference genes

Usage

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

Arguments

eset

expression data with matched gene id of reference

project

project name used to distinguish different datasets

arrays

a logical value. If TRUE, the columns of the input data will be normalized to have the same quantiles.

method

deconvolution method. must be "svr" or "lsei"

perm

permutation to run svr

reference

immune cell gene matrix; eg lm22, lm6 or can be generate using generateRef/generateRef_rnaseq

scale_reference

a logical value indicating whether the reference be scaled or not. If TRUE, the value in reference file will be centered and scaled in row direction.

absolute.mode

absolute.mode, default is FALSE

abs.method

abs.method, default is sig.score

Author(s)

Dongqiang Zeng

Rongfang Shen

Examples

# Loading TCGA-STAD expresion data(raw count matrix)
data(eset_stad, package = "IOBR")
eset <- count2tpm(countMat = eset_stad, source = "local", idType = "ensembl")
deconvo_ref(eset = eset, reference = lm22)

IOBR/IOBR documentation built on March 23, 2024, 9:37 a.m.