filterExperimentByFrequency: Filter experiment by frequency

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

Filter experiment by frequency

Description

Helper function for experiments filtering

Usage

filterExperimentByFrequency(
  experiment,
  carrier_frequency = FALSE,
  lower_frequency_cutoff = NULL,
  upper_frequency_cutoff = NULL
)

## S3 method for class 'matrix'
filterExperimentByFrequency(
  experiment,
  carrier_frequency = FALSE,
  lower_frequency_cutoff = NULL,
  upper_frequency_cutoff = NULL
)

## S3 method for class 'SummarizedExperiment'
filterExperimentByFrequency(
  experiment,
  carrier_frequency = FALSE,
  lower_frequency_cutoff = NULL,
  upper_frequency_cutoff = NULL
)

Arguments

experiment	Matrix or SummarizedExperiment object.
carrier_frequency	Logical flag indicating if carrier frequency should be returned.
lower_frequency_cutoff	Positive number or NULL. Numbers greater than 1 are interpreted as number of feature occurrences, numbers between 0 and 1 as fractions.
upper_frequency_cutoff	Positive number or NULL. Numbers greater than 1 are interpreted as number of feature occurrences, numbers between 0 and 1 as fractions.

Value

Filtered experiment matrix.

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