Library size normalize
CID.Normalize normalizes the expression matrix to the mean library size.
CID.Normalize(E)
E |
Expression matrix |
Normalized expression matrix where each cell sums to the mean total counts
## Not run: # download single cell data for classification file.dir = "https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_v3/" file = "pbmc_1k_v3_filtered_feature_bc_matrix.h5" download.file(paste0(file.dir, file), "Ex.h5") # load data, process with Seurat library(Seurat) E = Read10X_h5(filename = "Ex.h5") # observe average total counts mean(Matrix::colSums(E)) # run normalization E_norm = CID.Normalize(E) # check normalization kmu = mean(Matrix::colSums(E_norm)) head(kmu) ## End(Not run)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.