compute_abundance: Computes the abundance for every integration event in the...

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

Description

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maturing Abundance is obtained for every integration event by calculating the ratio between the single value and the total value for the given group.

Usage

compute_abundance(
  x,
  columns = "Value",
  percentage = TRUE,
  key = "CompleteAmplificationID",
  keep_totals = FALSE
)

Arguments

x	An integration matrix - aka a data frame that includes the mandatory_IS_vars() as columns. The matrix can either be aggregated (via aggregate_values_by_key()) or not.
columns	A character vector of column names to process, must be numeric or integer columns
percentage	Add abundance as percentage?
key	The key to group by when calculating totals
keep_totals	A value between TRUE, FALSE or df. If TRUE, the intermediate totals for each group will be kept in the output data frame as a dedicated column with a trailing "_tot". If FALSE, totals won't be included in the output data frame. If df, the totals are returned to the user as a separate data frame, together with the abundance data frame.

Details

Abundance will be computed upon the user selected columns in the columns parameter. For each column a corresponding relative abundance column (and optionally a percentage abundance column) will be produced.

Value

Either a single data frame with computed abundance values or a list of 2 data frames (abundance_df, quant_totals)

See Also

Other Analysis functions: CIS_grubbs(), comparison_matrix(), cumulative_count_union(), sample_statistics(), separate_quant_matrices(), threshold_filter(), top_integrations()

Examples

path <- system.file("extdata", "ex_annotated_ISMatrix.tsv.xz",
    package = "ISAnalytics"
)
matrix <- import_single_Vispa2Matrix(path)

# Simple integration matrix - grouping by CompleteAmplificationID
abundance1 <- compute_abundance(matrix)
abundance1

# Keeping totals as a separate data frame
abundance2 <- compute_abundance(matrix, keep_totals = "df")
abundance2

ISAnalytics documentation built on April 9, 2021, 6:01 p.m.