generateRef_rnaseq: Generate reference gene matrix from DEGs result

In IOBR/IOBR: Immune Oncology Biological Research

Generate reference gene matrix from DEGs result

Description

Generate reference gene matrix from DEGs result

Usage

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

Arguments

dds	raw count data from RNA-seq
pheno	data frame or matrix;un-normalized counts of RNA-seq
mode	mode "oneVSothers" or "pairs"; two modes for identifying significantly differentially expressed genes
FDR	character vector; cell type class of the samples
dat	data frame or matrix; normalized transcript quantification data (like FPKM, TPM). Note: cell's median expression level of the identified probes will be the output of reference_matrix.

Author(s)

Rongfang Shen

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