as_sparse_matrix: Converts tidy integration matrices in the original sparse...

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Converts tidy integration matrices in the original sparse matrix form.

Description

This function is particularly useful when a sparse matrix structure is needed by a specific function (mainly from other packages).

Usage

as_sparse_matrix(
  x,
  single_value_col = "Value",
  fragmentEstimate = "fragmentEstimate",
  seqCount = "seqCount",
  barcodeCount = "barcodeCount",
  cellCount = "cellCount",
  ShsCount = "ShsCount",
  key = pcr_id_column()
)

Arguments

x	A single tidy integration matrix or a list of integration matrices. Supports also multi-quantification matrices obtained via comparison_matrix
single_value_col	Name of the column containing the values when providing a single-quantification matrix
fragmentEstimate	For multi-quantification matrix support: the name of the fragment estimate values column
seqCount	For multi-quantification matrix support: the name of the sequence count values column
barcodeCount	For multi-quantification matrix support: the name of the barcode count values column
cellCount	For multi-quantification matrix support: the name of the cell count values column
ShsCount	For multi-quantification matrix support: the name of the Shs Count values column
key	The name of the sample identifier fields (for aggregated matrices can be a vector with more than 1 element)

Value

Depending on input, 2 possible outputs:

• A single sparse matrix (data frame) if input is a single quantification matrix

• A list of sparse matrices divided by quantification if input is a single multi-quantification matrix or a list of matrices

See Also

Other Utilities: comparison_matrix(), enable_progress_bars(), export_ISA_settings(), generate_Vispa2_launch_AF(), generate_blank_association_file(), generate_default_folder_structure(), import_ISA_settings(), separate_quant_matrices(), transform_columns()

Examples

data("integration_matrices", package = "ISAnalytics")
sparse <- as_sparse_matrix(integration_matrices)

calabrialab/ISAnalytics documentation built on Nov. 2, 2023, 8:57 p.m.