DESeqDataSet built in the lesson "De las cuentas de RNA-seq a la
exploración de datos" (intro_RNAseq_es), ready to be used
as the starting point of later lessons.
Format
A DESeqDataSet with 13,596 genes and 99 samples. Its
colData is metadata_cleaned plus a Volunteer_ID column.
Details
This object is not installed with the package because of its size: get
it with dds <- download_data("dds") (see download_data).
Steps: DESeqDataSetFromTximport() from filtered_txi and
metadata_cleaned with design ~ Cell_type + Group (reference
levels monocyte and Ctrl), removal of genes with fewer than 10
reads in at least 10 samples, and estimateSizeFactors().
Requires the DESeq2 package (Bioconductor) to be used.
The script that generates it is data-raw/lesson2_checkpoints.R.
Examples
if (FALSE) { # interactive() && requireNamespace("DESeq2", quietly = TRUE)
library(DESeq2)
dds <- download_data("dds")
dds
design(dds)
}