Normalize raw datasets to column sums
This function normalizes data to account for total gene expression across a cell.
normalize( object, chunk = 1000, format.type = "10X", remove.missing = TRUE, verbose = TRUE )
object |
|
chunk |
size of chunks in hdf5 file. (default 1000) |
format.type |
string of HDF5 format (10X CellRanger by default). |
remove.missing |
Whether to remove cells not expressing any measured genes, and genes not expressed in any cells (if take.gene.union = TRUE, removes only genes not expressed in any dataset) (default TRUE). |
verbose |
Print progress bar/messages (TRUE by default) |
liger object with norm.data slot set.
# Demonstration using matrices with randomly generated numbers Y <- matrix(runif(5000,0,2), 10,500) Z <- matrix(runif(5000,0,2), 10,500) ligerex <- createLiger(list(y_set = Y, z_set = Z)) ligerex <- normalize(ligerex)
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