sample_statistics {ISAnalytics} | R Documentation

## Computes user specified functions on numerical columns and updates the metadata data frame accordingly.

### Description

The function operates on a data frame by grouping the content by the sample key and computing every function specified on every column in the `value_columns` parameter. After that the metadata data frame is updated by including the computed results as columns for the corresponding key. For this reason it's required that both `x` and `metadata` have the same sample key, and it's particularly important if the user is working with previously aggregated data. For example:

    ### Importing association file and matrices
    path_AF <- system.file("extdata", "ex_association_file.tsv",
    package = "ISAnalytics")
    root_correct <- system.file("extdata", "fs.zip",
    package = "ISAnalytics")
    root_correct <- unzip_file_system(root_correct, "fs")

    association_file <- import_association_file(path_AF, root_correct)
    matrices <- import_parallel_Vispa2Matrices_auto(
    association_file = association_file , root = NULL,
    quantification_type = c("seqCount","fragmentEstimate"),
    matrix_type = "annotated", workers = 2, patterns = NULL,
    matching_opt = "ANY", dates_format = "dmy")

    ### Aggregating data (both by same key)
    aggreggated_x <- aggregate_values_by_key(matrices$seqCount,
    association_file)
    aggregated_meta <- aggregate_metadata(association_file)

    ### Sample statistics
    sample_stats <- sample_statistics(x = aggregated_x,
    metadata = aggregated_meta,
    sample_key = c("SubjectID", "CellMarker","Tissue", "TimePoint"))

### Usage

    sample_statistics(
      x,
      metadata,
      sample_key = "CompleteAmplificationID",
      value_columns = "Value",
      functions = default_stats()
    )

### Arguments

`x` | A data frame
`metadata` | The metadata data frame
`sample_key` | Character vector representing the key for identifying a sample
`value_columns` | THe name of the columns to be computed, must be numeric or integer
`functions` | A named list of function or purrr-style lambdas

### Value

A list with modified x and metadata data frames

### See Also

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

### Examples

    op <- options(ISAnalytics.widgets = FALSE)

    path_AF <- system.file("extdata", "ex_association_file.tsv",
        package = "ISAnalytics"
    )
    root_correct <- system.file("extdata", "fs.zip",
        package = "ISAnalytics"
    )
    root_correct <- unzip_file_system(root_correct, "fs")

    association_file <- import_association_file(path_AF, root_correct,
        dates_format = "dmy"
    )
    matrices <- import_parallel_Vispa2Matrices_auto(
        association_file = association_file, root = NULL,
        quantification_type = c("seqCount", "fragmentEstimate"),
        matrix_type = "annotated", workers = 2, patterns = NULL,
        matching_opt = "ANY", multi_quant_matrix = FALSE
    )

    stats <- sample_statistics(matrices$seqCount, association_file)
    options(op)

[Package ISAnalytics version 1.2.1 Index]