compute_abundance {ISAnalytics} | R Documentation

## Computes the abundance for every integration event in the input data frame.

### Description

Abundance is obtained for every integration event by calculating the ratio between the single value and the total value for the given group.

### Usage

    compute_abundance(
      x,
      columns = "Value",
      percentage = TRUE,
      key = "CompleteAmplificationID",
      keep_totals = FALSE
    )

### Arguments

`x` | An integration matrix - aka a data frame that includes the `mandatory_IS_vars()` as columns. The matrix can either be aggregated (via `aggregate_values_by_key()`) or not.
`columns` | A character vector of column names to process, must be numeric or integer columns
`percentage` | Add abundance as percentage?
`key` | The key to group by when calculating totals
`keep_totals` | A value between `TRUE`, `FALSE` or `df`. If `TRUE`, the intermediate totals for each group will be kept in the output data frame as a dedicated column with a trailing "_tot". If `FALSE`, totals won't be included in the output data frame. If `df`, the totals are returned to the user as a separate data frame, together with the abundance data frame.

### Details

Abundance will be computed upon the user selected columns in the `columns` parameter. For each column a corresponding relative abundance column (and optionally a percentage abundance column) will be produced.

### Value

Either a single data frame with computed abundance values or a list of 2 data frames (abundance_df, quant_totals)

### See Also

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

### Examples

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

    # Simple integration matrix - grouping by CompleteAmplificationID
    abundance1 <- compute_abundance(matrix)
    abundance1

    # Keeping totals as a separate data frame
    abundance2 <- compute_abundance(matrix, keep_totals = "df")
    abundance2

[Package ISAnalytics version 1.2.1 Index]