cumulative_is {ISAnalytics} | R Documentation

## Expands integration matrix with the cumulative is union over time.

### Description

Given an input integration matrix that can be grouped over time, this function adds integrations in groups assuming that if an integration is observed at time point "t" then it is also observed in time point "t+1".

### Usage

    cumulative_is(
      x,
      key = c("SubjectID", "CellMarker", "Tissue", "TimePoint"),
      timepoint_col = "TimePoint",
      include_tp_zero = FALSE,
      keep_og_is = TRUE,
      expand = FALSE
    )

### Arguments

`x` | An integration matrix, ideally aggregated via `aggregate_values_by_key()`
`key` | The aggregation key used
`timepoint_col` | The name of the time point column
`include_tp_zero` | Should time point 0 be included?
`keep_og_is` | Keep original set of integrations as a separate column?
`expand` | If `FALSE`, for each group, the set of integration sites is returned in a separate column as a nested table, otherwise the resulting column is unnested.

### Value

A data frame

### See Also

Other Analysis functions: `CIS_grubbs()`, `comparison_matrix()`, `compute_abundance()`, `cumulative_count_union()`, `is_sharing()`, `iss_source()`, `purity_filter()`, `sample_statistics()`, `separate_quant_matrices()`, `threshold_filter()`, `top_integrations()`

### Examples

    data("integration_matrices", package = "ISAnalytics")
    data("association_file", package = "ISAnalytics")
    aggreg <- aggregate_values_by_key(
        x = integration_matrices,
        association_file = association_file,
        value_cols = c("seqCount", "fragmentEstimate")
    )
    cumulated_is <- cumulative_is(aggreg)
    cumulated_is

[Package ISAnalytics version 1.4.3 Index]