deconvo_quantiseq: Deconvoluting micrornvironment using the quanTIseq technique

In IOBR/IOBR: Immune Oncology Biological Research

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. 27, 2024, 6:44 p.m.