mutate_median_intensity: Add Median Intensity to mass_dataset Object

In tidymass/massdataset: massdataset

Add Median Intensity to mass_dataset Object

Description

This function calculates the median intensity for each variable in the mass_dataset object based on the specified samples and adds it as a new column to the variable information.

Usage

mutate_median_intensity(object, according_to_samples = "all", na.rm = TRUE)

Arguments

object	A mass_dataset object.
according_to_samples	A character vector specifying the samples to consider for the median calculation. Default is "all".
na.rm	Logical, whether to remove NA values before calculating the median. Default is TRUE.

Value

A modified mass_dataset object with added median intensity information.

Author(s)

Xiaotao Shen [e-mail]

Examples

data("expression_data")
data("sample_info")
data("variable_info")

object =
  create_mass_dataset(
    expression_data = expression_data,
    sample_info = sample_info,
    variable_info = variable_info,
  )

object

##calculate median intensity according to all the samples
object2 =
  mutate_median_intensity(object = object, na.rm = TRUE)

object2

head(extract_variable_info(object))
head(extract_variable_info(object2))

##calculate median intensity according to only QC samples
object3 =
  mutate_median_intensity(object = object2,
                according_to_samples =
              get_sample_id(object)[extract_sample_info(object)$class == "QC"])

object3

head(extract_variable_info(object3))

tidymass/massdataset documentation built on Jan. 30, 2024, 2:55 p.m.