comparison_matrix: Obtain a single integration matrix from individual...

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

Obtain a single integration matrix from individual quantification matrices.

Description

Takes a list of integration matrices referring to different quantification types and merges them into a single data frame with multiple value columns, each renamed according to their quantification type of reference.

Usage

comparison_matrix(
  x,
  fragmentEstimate = "fragmentEstimate",
  seqCount = "seqCount",
  barcodeCount = "barcodeCount",
  cellCount = "cellCount",
  ShsCount = "ShsCount",
  value_col_name = "Value"
)

Arguments

x	A named list of integration matrices, ideally obtained via import_parallel_Vispa2Matrices. Names must be quantification types in quantification_types().
fragmentEstimate	The name of the output column for fragment estimate values
seqCount	The name of the output column for sequence count values
barcodeCount	The name of the output column for barcode count values
cellCount	The name of the output column for cell count values
ShsCount	The name of the output column for Shs count values
value_col_name	Name of the column containing the corresponding values in the single matrices

Value

A single data frame

See Also

quantification_types

Other Utilities: as_sparse_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

sc <- tibble::tribble(
    ~chr, ~integration_locus, ~strand, ~CompleteAmplificationID, ~Value,
    "1", 45324, "+", "ID1", 543,
    "2", 52423, "-", "ID1", 42,
    "6", 54623, "-", "ID2", 67,
    "X", 12314, "+", "ID3", 8
)
fe <- tibble::tribble(
    ~chr, ~integration_locus, ~strand, ~CompleteAmplificationID, ~Value,
    "1", 45324, "+", "ID1", 56.76,
    "2", 52423, "-", "ID1", 78.32,
    "6", 54623, "-", "ID2", 123.45,
    "X", 12314, "+", "ID3", 5.34
)
comparison_matrix(list(
    fragmentEstimate = fe,
    seqCount = sc
))

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