sample_statistics: Computes user specified functions on numerical columns and...

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

Computes user specified functions on numerical columns and updates the metadata data frame accordingly.

Description

The function operates on a data frame by grouping the content by the sample key and computing every function specified on every column in the value_columns parameter. After that the metadata data frame is updated by including the computed results as columns for the corresponding key. For this reason it's required that both x and metadata have the same sample key, and it's particularly important if the user is working with previously aggregated data. For example:

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")
)
aggreg_meta <- aggregate_metadata(association_file = association_file)

sample_stats <- sample_statistics(x = aggreg,
metadata = aggreg_meta,
value_columns = c("seqCount", "fragmentEstimate"),
sample_key = c("SubjectID", "CellMarker","Tissue", "TimePoint"))

Usage

sample_statistics(
  x,
  metadata,
  sample_key = "CompleteAmplificationID",
  value_columns = "Value",
  functions = default_stats(),
  add_integrations_count = TRUE
)

Arguments

x	A data frame
metadata	The metadata data frame
sample_key	Character vector representing the key for identifying a sample
value_columns	The name of the columns to be computed, must be numeric or integer
functions	A named list of function or purrr-style lambdas
add_integrations_count	Add the count of distinct integration sites for each group? Can be computed only if x contains the mandatory columns mandatory_IS_vars()

Value

A list with modified x and metadata data frames

Required tags

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

• All columns declared in mandatory_IS_vars()

These are checked only if add_integrations_count = TRUE.

See Also

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

Examples

data("integration_matrices", package = "ISAnalytics")
data("association_file", package = "ISAnalytics")
stats <- sample_statistics(
    x = integration_matrices,
    metadata = association_file,
    value_columns = c("seqCount", "fragmentEstimate")
)
stats

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