generateRef: Generate Reference signature matrix

In IOBR/IOBR: Immune Oncology Biological Research

Generate Reference signature matrix

Description

Generate Reference signature matrix

Usage

generateRef(dds, pheno, FDR = 0.05, dat, method = "limma")

Arguments

dds	raw count data from RNA-seq; Necessary if used the method DESeq2
pheno	character vector; cell type class of the samples
FDR	numeric; genes with BH adjust p value < FDR are considered significant.
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.
method	limma or DESeq2

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