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

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

Description

\lifecycle

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

Usage

as_sparse_matrix(
  x,
  fragmentEstimate = "fragmentEstimate",
  seqCount = "seqCount",
  barcodeCount = "barcodeCount",
  cellCount = "cellCount",
  ShsCount = "ShsCount"
)

Arguments

x	A single tidy integration matrix or a list of integration matrices. Supports also multi-quantification matrices obtained via comparison_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

Value

Depending on input, 2 possible outputs:

• A single sparce matrix (tibble) if input is a single quantification matrix

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

See Also

Other Utility functions: generate_Vispa2_launch_AF(), generate_blank_association_file(), unzip_file_system()

Examples

path <- system.file("extdata", "ex_annotated_ISMatrix.tsv.xz",
    package = "ISAnalytics"
)
matrix <- import_single_Vispa2Matrix(path)
sparse <- as_sparse_matrix(matrix)

ISAnalytics documentation built on April 9, 2021, 6:01 p.m.