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

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

Description

\lifecycle

maturing Takes a list of integration matrices referring to different qunatification types and merges them in a single data frame that has 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"
)

Arguments

x	A named list of integration matrices, ideally obtained via import_parallel_Vispa2Matrices_interactive or import_parallel_Vispa2Matrices_auto. Names must be 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

A tibble

See Also

quantification_types

Other Analysis functions: CIS_grubbs(), compute_abundance(), cumulative_count_union(), sample_statistics(), separate_quant_matrices(), threshold_filter(), top_integrations()

Examples

op <- options("ISAnalytics.widgets" = FALSE)
path <- system.file("extdata", "ex_association_file.tsv",
    package = "ISAnalytics"
)
root_pth <- system.file("extdata", "fs.zip", package = "ISAnalytics")
root <- unzip_file_system(root_pth, "fs")
matrices <- import_parallel_Vispa2Matrices_auto(
   association_file = path, root = root,
   quantification_type =  c("fragmentEstimate", "seqCount"),
   matrix_type =  "annotated", workers = 2, patterns =  NULL,
   matching_opt =  "ANY",
   dates_format = "dmy", multi_quant_matrix = FALSE
)
total_matrix <- comparison_matrix(matrices)
options(op)

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