make_dds: Make DESeqDataSet from counts matrix and metadata

In RNAseqQC: Quality Control for RNA-Seq Data

Make DESeqDataSet from counts matrix and metadata

Description

Make DESeqDataSet from counts matrix and metadata

Usage

make_dds(counts, metadata, ah_record, design = ~1)

Arguments

counts	The genes x samples counts matrix with row names. At least one row name must be an ENSEMBL gene ID, since gene annotation is done via the ENSEMBL database.
metadata	data.frame of sample information. Order of rows corresponds to the order of columns in the counts matrix.
ah_record	ID of AnnotationHub record used to retrieve an EnsDb object.
design	The design formula specified in DESeqDataSet() To view all valid record IDs, run library(AnnotationHub) mcols(AnnotationHub()) %>% as_tibble(rownames="ah_record") %>% filter(rdataclass=="EnsDb")

Value

A DESeq2::DESeqDataSet object containing the counts matrix and metadata.

Examples

library("DESeq2")
count_mat <- counts(T47D)
meta <- data.frame(colData(T47D))
dds <- make_dds(counts = count_mat, metadata = meta, ah_record = "AH89426")

RNAseqQC documentation built on July 1, 2024, 9:07 a.m.