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Load in data directly from R objects.

load_r_data.Rd

This function loads in data directly from R objects.

Usage

load_r_data(
  object,
  counts,
  obs,
  var,
  sc_qc_param = params_sc_min_quality(),
  batch_size = 1000L,
  streaming = TRUE,
  .verbose = TRUE
)

Arguments

object

SingleCells class.

counts

Sparse matrix. The cells represent the rows, the genes the indices. Needs to be "dgRMatrix".

obs

data.table. The data.table representing the observations, i.e., cell information.

var

data.table. The data.table representing the features, i.e., the feature information.

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.