calculate_sig_score_pca: Calculating signature score using PCA method

In IOBR/IOBR: Immune Oncology Biological Research

Calculating signature score using PCA method

Description

Calculating signature score using PCA method

Usage

calculate_sig_score_pca(
  pdata = NULL,
  eset,
  signature,
  mini_gene_count = 3,
  column_of_sample = "ID",
  adjust_eset = FALSE
)

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	normalized transcriptomic data: normalized (CPM, TPM, RPKM, FPKM, etc.), Gene expression data should be scale before signature score estimation
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.
adjust_eset	remove variables with missing value, sd =0, and Inf value

Value

signature scores for gene sets; signatures in columns, samples in rows

Author(s)

Dongqiang Zeng

Examples

# Loading TCGA-STAD expresion data(raw count matrix)
data("eset_stad", package = "IOBR")
# transform count data to tpm
eset <- count2tpm(eset_stad, idType = "ensembl")
# signature score estimation using PCA method
calculate_sig_score_pca(eset = eset, signature = signature_tme)

IOBR/IOBR documentation built on Nov. 27, 2024, 6:44 p.m.