filterByFrequency: Filter MiDAS object by frequency

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

Filter MiDAS object by frequency

Description

Filter MiDAS object by frequency

Usage

filterByFrequency(
  object,
  experiment,
  lower_frequency_cutoff = NULL,
  upper_frequency_cutoff = NULL,
  carrier_frequency = FALSE
)

Arguments

object	MiDAS object.
experiment	String specifying experiment.
lower_frequency_cutoff	Number giving lower frequency threshold. Numbers greater than 1 are interpreted as the number of feature occurrences, numbers between 0 and 1 as fractions.
upper_frequency_cutoff	Number giving upper frequency threshold. Numbers greater than 1 are interpreted as the number of feature occurrences, numbers between 0 and 1 as fractions.
carrier_frequency	Logical flag indicating if carrier frequency should be returned.

Value

Filtered MiDAS object.

Examples

filterByFrequency(object = MiDAS_tut_object, 
                  experiment = "hla_alleles",
                  lower_frequency_cutoff = 0.05,
                  upper_frequency_cutoff = 0.95,
                  carrier_frequency = TRUE)

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