comparison_matrix {ISAnalytics} | R Documentation

## obtain a single integration matrix from individual quantification matrices.

### Description

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)

[Package ISAnalytics version 1.2.1 Index]