tmescore_estimation_helper: Calculating TMEscore using PCR data

In DongqiangZeng0808/TMEscore: Estimating Tumor Microenvironment Score

Calculating TMEscore using PCR data

Description

Calculating TMEscore using PCR data

Usage

tmescore_estimation_helper(
  pdata = NULL,
  eset,
  signature = NULL,
  mini_gene_count = 2,
  column_of_sample = "ID",
  replace_na = FALSE,
  scale = FALSE,
  method = "mean",
  adjust_eset = FALSE,
  log2trans = FALSE,
  save_data = FALSE,
  file_name = NULL
)

Arguments

pdata	phenotype data of input sample; if phenotype data is NULL, create a data frame with 'Index' and 'ID' contain column names of eset
eset	normalizaed transcriptomic data: normalized (CPM, TPM, RPKM, FPKM, etc.)
signature	List of gene signatures
mini_gene_count	filter out signatures with genes less than minimal gene in expression set;
column_of_sample	Defines in which column of pdata the sample identifier can be found
replace_na	default is FALSE
scale	default is FALSE
method	default is TRUE
adjust_eset	remove variables with missing value, sd =0, and Inf value
log2trans	default is FALSE
save_data	default is FALSE
file_name	default is null

Value

data frame with pdata and signature scores for gene sets; signatures in columns, samples in rows

Author(s)

Dongqiang Zeng

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