deconvo_timer: Deconvoluting using the TIMER technique

In IOBR/IOBR: Immune Oncology Biological Research

Deconvoluting using the TIMER technique

Description

This function performs deconvolution of immune cell fractions using the TIMER (Tumor Immune Estimation Resource) technique. Unlike the other methods, TIMER needs the specification of the cancer type for each sample.

Usage

deconvo_timer(eset, project = NULL, indications = NULL)

Arguments

eset	gene matrix
project	default is NULL, project name used to distinguish different data sets
indications	a n-vector giving and indication string (e.g. 'brca') for each sample. Accepted indications are 'kich', 'blca', 'brca', 'cesc', 'gbm', 'hnsc', 'kirp', 'lgg','lihc', 'luad', 'lusc', 'prad', 'sarc', 'pcpg', 'paad', 'tgct','ucec', 'ov', 'skcm', 'dlbc', 'kirc', 'acc', 'meso', 'thca','uvm', 'ucs', 'thym', 'esca', 'stad', 'read', 'coad', 'chol'

Value

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

Examples

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

IOBR/IOBR documentation built on April 3, 2025, 2:19 p.m.