tmescore: Calculate TMEscore

In DongqiangZeng0808/TMEscore: Estimating Tumor Microenvironment Score

Calculate TMEscore

Description

Calculate TMEscore

Usage

tmescore(
  eset,
  pdata = NULL,
  column_of_sample = "ID",
  method = "PCA",
  print_gene_pro = FALSE,
  classify = FALSE
)

Arguments

eset	normalized expression data use function: scale(); with human gene symbol in rows and patient identifier in columns;
pdata	phenotype data with patient identifier or other clinical data in columns; the number of rows in pdata should be equal to the number of columns in eset
column_of_sample	Defines in which column of pdata the sample identifier can be found.
method	use PCA (default) or z-score function to calculate TMEscore
print_gene_pro	print signature gene propotion, default is FALSE
classify	classifying TMEscore into two groups using survival data and function of suvmmer.

Value

pdata with TMEscoreA, TMEscoreB and TMEscore

Author(s)

Dongqiang Zeng

Examples

tmescore<-tmescore(eset = eset_stad,pdata = pdata_stad,column_of_sample = "ID")

DongqiangZeng0808/TMEscore documentation built on Feb. 7, 2023, 5:13 a.m.