cumulative_count_union: Integrations cumulative count in time by sample

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

Integrations cumulative count in time by sample

Description

This function was deprecated in favour of a single function, please use cumulative_is instead.

Usage

cumulative_count_union(
  x,
  association_file = NULL,
  timepoint_column = "TimePoint",
  key = c("SubjectID", "CellMarker", "Tissue", "TimePoint"),
  include_tp_zero = FALSE,
  zero = "0000",
  aggregate = FALSE,
  ...
)

Arguments

x	A simple integration matrix or an aggregated matrix (see details)
association_file	NULL or the association file for x if aggregate is set to TRUE
timepoint_column	What is the name of the time point column?
key	The aggregation key - must always contain the timepoint_column
include_tp_zero	Include timepoint 0?
zero	How is 0 coded in the data frame?
aggregate	Should x be aggregated?
...	Additional parameters to pass to aggregate_values_by_key

Value

A data frame

Examples

## Not run: 
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")
)
cumulative_count <- cumulative_count_union(aggreg)
cumulative_count

## End(Not run)

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