Harmony code

[nsohail19]

We run PCA on top of the harmony reduction that is calculated during the IntegrateLayers() step of HarmonyIntegration. Removing this step should fix the code (where it will just run the SCTransform method)

Either fix this or recommend using the simpler RunHarmony() method:

# Normalize, HVG, scale
seurat <- NormalizeData(seurat)
seurat <- FindVariableFeatures(seurat)
seurat <- ScaleData(seurat)

# PCA
seurat <- RunPCA(seurat)

# Run Harmony
seurat <- RunHarmony(seurat, 
                     group.by.vars = "Donor", 
                     reduction = "pca", 
                     dims.use = 1:30,
                     assay.use = "RNA", 
                     reduction.save = "harmony")

# UMAP
seurat <- RunUMAP(seurat,
                  reduction = "harmony",
                  dims = 1:30)

# Clusters
seurat <- FindNeighbors(seurat,
                        reduction = "harmony",
                        dims = 1:30)
seurat <- FindClusters(seurat,
                       resolution = 0.6)

[epartan]

I think this error was just in the scRNA template, not in the lesson. The lesson looks fine to me.