Estimate Size Factors for New Dataset Based on Training Geometric Means

This function estimates size factors for a new dataset based on the geometric means from a training dataset. It can take either a counts table with metadata or a DESeqDataSet object.

Usage

normalizeTestDataset(counts = NULL, metadata = NULL, dds = NULL, geom)

Arguments

counts: A data frame or matrix containing raw unnormalized RNA-Seq gene counts. Columns are samples, rows are genes.
metadata: A data frame containing sample metadata. Required if counts is provided.
dds: A DESeqDataSet object. If provided, counts and metadata are ignored.
geom: A named numeric vector containing the geometric means of the training dataset.

Value

A DESeqDataSet object with estimated size factors.

Examples

if (FALSE) { # \dontrun{
geom <- readRDS("./SVM_GD2_dashboard/data/geom_train_data.Rds")

counts <-
  read.table("SVM_GD2_dashboard/data/datasets/rus_cell_lines_counts.tsv",
             sep = "\t", header = TRUE)
metadata <-
  read.table("SVM_GD2_dashboard/data/datasets/rus_cell_lines_metadata.tsv",
             sep = "\t", header = TRUE)

dds <- normalizeTestDataset(counts = counts, metadata = metadata, geom = geom)
} # }