Calculate experiment's features frequencies — getExperimentFrequencies • midasHLA

getExperimentFrequencies calculate features frequencies.

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

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

# S3 method for 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.