This function retrieves counts from a number of methods that are available for normalisation, with the default of limma-voomLmFit.
Usage
compute_single_de(
data = NULL,
treatment_samples = NULL,
control_samples = NULL,
method = NULL,
batch = 1,
k = 2,
spikes = NULL
)Arguments
- data
A tidyseurat object merged with metadata. Must contain columns "Well_ID", "Row", "Column"
- treatment_samples
Value in the column "combined_id" representing replicates of treatment samples in the data
- control_samples
Value in the column "combined_id" representing replicates of control samples in the data
- method
One of "Seurat_wilcox", "DESeq2", "edgeR", "RUVg", "RUVs", "RUVr", "limma_voom"
- batch
Either empty, a single value, or a vector corresponding to the number of samples
- k
Parameter k for RUVSeq methods, check RUVSeq tutorial
- spikes
List of genes to use as spike controls
Examples
data(mini_mac)
treatment_samples="Staurosporine_0.1"
control_samples<-"DMSO_0"
top_table <- compute_single_de(mini_mac, treatment_samples, control_samples, method = "limma_voom")