getExperimentFrequencies: Calculate experiment's features frequencies

In Genentech/midasHLA: R package for immunogenomics data handling and association analysis

Calculate experiment's features frequencies

Description

getExperimentFrequencies calculate features frequencies.

Usage

getExperimentFrequencies(
  experiment,
  pop_mul = NULL,
  carrier_frequency = FALSE,
  ref = NULL
)

## S3 method for class 'matrix'
getExperimentFrequencies(
  experiment,
  pop_mul = NULL,
  carrier_frequency = FALSE,
  ref = NULL
)

## S3 method for class 'SummarizedExperiment'
getExperimentFrequencies(
  experiment,
  pop_mul = NULL,
  carrier_frequency = FALSE,
  ref = NULL
)

Arguments

experiment	Matrix or SummarizedExperiment object.
pop_mul	Number by which number of samples should be multiplied to get the population size.
carrier_frequency	Logical flag indicating if carrier frequency should be returned.
ref	Wide format data frame with first column named "var" holding features matching experiment and specific populations frequencies in following columns. See getReferenceFrequencies for more details.

Value

Data frame with each row holding specific variable, it's count and frequency.

Genentech/midasHLA documentation built on Feb. 12, 2024, 9:38 a.m.