combine_pd_eset: Title combine_pd_eset

In IOBR/IOBR: Immune Oncology Biological Research

Title combine_pd_eset

Description

combine_pd_eset combines the expression set (eset) with phenotype data (pdata).

Usage

combine_pd_eset(
  eset,
  pdata,
  id_pdata = "ID",
  feas = NULL,
  feature_manipulation = TRUE,
  scale = TRUE,
  choose_who_when_duplicate = "eset"
)

Arguments

eset	Expression set matrix or data frame.
pdata	Phenotype data.
id_pdata	String indicating the column name in pdata that corresponds to the eset column.
feas	Vector of feature names to include in the combined dataset. Default is NULL, which includes all features.
feature_manipulation	Logical value indicating whether to perform feature manipulation on the data. Default is TRUE.
scale	Logical value indicating whether to scale the expression set. Default is TRUE.
choose_who_when_duplicate	String indicating the preference when encountering duplicate IDs in pdata and eset.

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")
colnames(eset) <- substring(colnames(eset), 1, 12)
# Loading TCGA-STAD microenvironment signature data
data("sig_stad", package = "IOBR")
eset <- count2tpm(eset_stad)
colnames(eset) <- substring(colnames(eset), 1, 12)
input <- combine_pd_eset(eset = eset, pdata = sig_stad, feas = unique(unlist(signature_collection)))

IOBR/IOBR documentation built on April 4, 2024, 1:07 a.m.