cash-proDAFit-method: Fluent use of accessor methods

In proDA: Differential Abundance Analysis of Label-Free Mass Spectrometry Data

Description

The 'proDAFit' object overwrites the dollar function to make it easy to call functions to access values inside the object. This has the advantage that it is very easy to discover the relevant methods but nonetheless have an isolated implementation. Unlike the `@` operator which directly accesses the underlying implementation, the `$` operator only exposes a limited set of functions

• abundances

• hyper_parameters

• feature_parameters

• coefficients

• convergence

• design

• reference_level

• result_names

• coefficient_variance_matrices

• colData

• rowData

Usage

## S3 method for class 'proDAFit'
.DollarNames(x, pattern = "")

## S4 method for signature 'proDAFit'
x$name

## S4 replacement method for signature 'proDAFit'
x$name <- value

Arguments

x	an object of class 'proDAFit' produced by proDA()
pattern	the regex pattern that is provided by the IDE
name	one of the functions listed above
value	Warning: modifying the content of a 'proDAFit' object is not allowed

Value

whatever the function called name returns.

See Also

accessor_methods for more documentation on the accessor functions.

Examples

  syn_data <- generate_synthetic_data(n_proteins = 10)
  fit <- proDA(syn_data$Y, design = syn_data$groups)

  # The two styles are identical
  design(fit)
  fit$design

  # More functions
  fit$abundances

proDA documentation built on Nov. 8, 2020, 5:01 p.m.