deconvo_timer: Deconvoluting using the TIMER technique Unlike the other...

In IOBR/IOBR: Immune Oncology Biological Research

Deconvoluting using the TIMER technique Unlike the other methods, TIMER needs the specification of the cancer type for each sample.

Description

Deconvoluting using the TIMER 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'

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 4, 2024, 1:07 a.m.