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Load in Seurat to SingleCells

load_seurat.Rd

This function takes a Seurat file and generates SingleCells class from it.

Usage

load_seurat(
  object,
  seurat,
  sc_qc_param = params_sc_min_quality(),
  batch_size = 1000L,
  streaming = TRUE,
  .verbose = TRUE
)

Arguments

object

SingleCells class.

seurat

Seurat class you want to transform.

sc_qc_param

List. Output of params_sc_min_quality(). A list with the following elements:

  • min_unique_genes - Integer. Minimum number of genes to be detected in the cell to be included.

  • min_lib_size - Integer. Minimum library size in the cell to be included.

  • min_cells - Integer. Minimum number of cells a gene needs to be detected to be included.

  • target_size - Float. Target size to normalise to. Defaults to 1e5.

batch_size

Integer. If streaming = TRUE, how many cells to process in one batch. Defaults to 1000L.

streaming

Boolean. Shall the data be streamed during the conversion of CSR to CSC. Defaults to TRUE and should be used for larger data sets.

.verbose

Boolean. Controls the verbosity of the function.

Value

It will populate the files on disk and return the class with updated shape information.