deconvo_quantiseq: Deconvoluting micrornvironment using the quanTIseq technique

View source: R/deconvo_tme.R

deconvo_quantiseqR Documentation

Deconvoluting micrornvironment using the quanTIseq technique

Description

This function performs deconvolution of the tumor microenvironment using the quanTIseq technique. It estimates the fraction of different cell types in the expression dataset.

Usage

deconvo_quantiseq(eset, project = NULL, tumor, arrays, scale_mrna)

Arguments

eset

gene expression data

project

default is NULL, project name used to distinguish different data sets

tumor

logistic variable

arrays

logistic variable, is data generated from microarray

scale_mrna

logistic variable

Value

A data frame with the estimated cell type fractions, with columns named according to the cell types and suffixed with "_quantiseq".

Examples

#' # Loading TCGA-STAD expresion data(raw count matrix)
data(eset_stad, package = "IOBR")
eset <- count2tpm(countMat = eset_stad, source = "local", idType = "ensembl")
deconvo_quantiseq(eset = eset, project = "stad", tumor = TRUE, arrays = FALSE, scale_mrna = FALSE)

IOBR/IOBR documentation built on Nov. 13, 2024, 5:22 a.m.