aggregate_metadata: Performs aggregation on metadata contained in the association...

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

Performs aggregation on metadata contained in the association file.

Description

Groups metadata by the specified grouping keys and returns a summary of info for each group. For more details on how to use this function: vignette("workflow_start", package = "ISAnalytics")

Usage

aggregate_metadata(
  association_file,
  grouping_keys = c("SubjectID", "CellMarker", "Tissue", "TimePoint"),
  aggregating_functions = default_meta_agg(),
  import_stats = lifecycle::deprecated()
)

Arguments

association_file	The imported association file (via import_association_file)
grouping_keys	A character vector of column names to form a grouping operation
aggregating_functions	A data frame containing specifications of the functions to be applied to columns in the association file during aggregation. It defaults to default_meta_agg. The structure of this data frame should be maintained if the user wishes to change the defaults.
import_stats	The import of VISPA2 stats has been moved to its dedicated function, see import_Vispa2_stats.

Value

An aggregated data frame

See Also

Other Data cleaning and pre-processing: aggregate_values_by_key(), compute_near_integrations(), default_meta_agg(), outlier_filter(), outliers_by_pool_fragments(), purity_filter(), realign_after_collisions(), remove_collisions(), threshold_filter()

Examples

data("association_file", package = "ISAnalytics")
aggreg_meta <- aggregate_metadata(
    association_file = association_file
)
head(aggreg_meta)

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