generateRef_rnaseq: Generate Reference Gene Matrix from RNA-seq DEGs

In IOBR: Immune Oncology Biological Research

Generate Reference Gene Matrix from RNA-seq DEGs

Description

Uses DESeq2 to identify differentially expressed genes and create a reference matrix from median expression levels across cell types.

Usage

generateRef_rnaseq(dds, pheno, mode = "oneVSothers", FDR = 0.05, dat)

Arguments

dds	Matrix. Raw count data from RNA-seq.
pheno	Character vector. Cell type classes.
mode	Character. DEG identification mode: '"oneVSothers"' or '"pairs"'. Default is '"oneVSothers"'.
FDR	Numeric. Threshold for adjusted p-values. Default is 0.05.
dat	Matrix. Normalized expression data (e.g., FPKM, TPM).

Value

List containing: - 'reference_matrix': Data frame of median expression for significant genes across cell types. - 'G': Optimal number of probes minimizing condition number. - 'condition_number': Minimum condition number. - 'whole_matrix': Full median expression matrix.

Author(s)

Rongfang Shen

Examples

dds <- matrix(rpois(200 * 10, lambda = 10), ncol = 10)
rownames(dds) <- paste("Gene", 1:200, sep = "_")
colnames(dds) <- paste("Sample", 1:10, sep = "_")
pheno <- sample(c("Type1", "Type2", "Type3"), 10, replace = TRUE)
dat <- matrix(rnorm(200 * 10), ncol = 10)
rownames(dat) <- rownames(dds)
colnames(dat) <- colnames(dds)

results <- generateRef_rnaseq(dds = dds, pheno = pheno, FDR = 0.05, dat = dat)

IOBR documentation built on May 30, 2026, 5:07 p.m.