cumulative_is {ISAnalytics}R Documentation

Expands integration matrix with the cumulative is union over time.

Description

[Experimental] 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]