iobr_deconvo_pieline: Title iobr_deconvo_pieline

In IOBR/IOBR: Immune Oncology Biological Research

Title iobr_deconvo_pieline

Description

The iobr_deconvo_pipeline function is used to perform a comprehensive TME (Tumor Microenvironment) analysis pipeline on a gene expression dataset. The pipeline includes TME deconvolution using various methods, calculation of signature scores, and the merging of TME and signature score results.

Usage

iobr_deconvo_pieline(
  eset,
  project,
  array,
  tumor_type,
  path = "1-TME",
  permutation = 1000
)

Arguments

eset	A gene expression dataset (e.g., expression set object) for TME analysis.
project	A character string specifying the name of the project or analysis.
array	A variable indicating the array type used in the gene expression dataset.
tumor_type	A character string specifying the type of tumor (e.g., "stad" for stomach adenocarcinoma).
path	A character string indicating the path for saving the output files. Default is "1-TME".
permutation	An integer specifying the number of permutations for TME deconvolution. Default is 1000.

Author(s)

Dongqiang Zeng

Examples

data("eset_stad", package = "IOBR")
eset <- count2tpm(eset_stad)
res <- iobr_deconvo_pieline(eset = eset, project = "STAD", array = FALSE, tumor_type = "stad", path = "1-TME", permutation = 1000)

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.