cumulative_is: Expands integration matrix with the cumulative IS union over...

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

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,
  counts = TRUE,
  keep_og_is = FALSE,
  expand = TRUE
)

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?
counts	Add cumulative counts? Logical
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

Required tags

The function will explicitly check for the presence of these tags:

• All columns declared in mandatory_IS_vars()

• Checks if the matrix is annotated by assessing presence of annotation_IS_vars()

See Also

Other Analysis functions: CIS_grubbs(), HSC_population_size_estimate(), compute_abundance(), gene_frequency_fisher(), is_sharing(), iss_source(), sample_statistics(), top_integrations(), top_targeted_genes()

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

calabrialab/ISAnalytics documentation built on Nov. 2, 2023, 8:57 p.m.