make_dds {RNAseqQC}

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")