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Analyses class and methods for handling statistical analysis data

Source: R/class_Analyses_StatisticAnalyses.R
StatisticAnalyses.Rd

The StatisticAnalyses class is used for tabular data statistical analysis.

Usage

StatisticAnalyses(
  analyses = NULL,
  classes = character(),
  concentrations = numeric(),
  ...
)

# S3 method for class 'StatisticAnalyses'
validate_object(x)

# S3 method for class 'StatisticAnalyses'
get_analysis_names(x)

# S3 method for class 'StatisticAnalyses'
get_analysis_classes(x)

# S3 method for class 'StatisticAnalyses'
set_analysis_classes(x, value)

# S3 method for class 'StatisticAnalyses'
get_concentrations(x)

# S3 method for class 'MassSpecAnalyses'
set_concentrations(x, value)

# S3 method for class 'StatisticAnalyses'
info(x)

# S3 method for class 'StatisticAnalyses'
add(x, value, ...)

# S3 method for class 'StatisticAnalyses'
remove(x, value)

# S3 method for class 'StatisticAnalyses'
x[i] <- value

# S3 method for class 'StatisticAnalyses'
x[[i]] <- value

# S3 method for class 'StatisticAnalyses'
plot_data(
  x,
  analyses = NULL,
  features = NULL,
  transpose = FALSE,
  interactive = TRUE,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorGroups = NULL,
  xTickLabelsShow = TRUE
)

Arguments

analyses

Character or numeric vector with names or indexes of analyses in the Analyses object.

classes

A character vector with the classes of the analyses.

concentrations

A numeric vector with the concentrations of the analyses.

...

Additional arguments passed to read.csv whet a file path is given.

x

A StatisticAnalyses object.

value

An object that highly depends on the method. Check the specific method documentation for details.

i

A character or numeric vector to perform subsetting. Check the specific method for details.

features

A numeric vector with the feature/variable indices (i.e., columns of data frame).

transpose

Logical, if TRUE the data is transposed (e.g., column names are used as legend when plotting).

interactive

Logical (length 1). When TRUE, the data is plotted interactively using plotly.

xLab

A string with the title for the x axis.

yLab

A string with the title for the y axis.

title

A string with the title.

colorGroups

A factor character vector with the color groups for the data.

xTickLabelsShow

Logical, if TRUE the x-axis tick labels are shown.

Value

A StatisticAnalyses object, which is a list with the following components:

  • analyses: A data.frame or matrix with the analyses data, where the row names are the analyses names and the column names are the variable names.

  • classes: A character vector with the classes of the analyses.

  • concentrations: A numeric vector with the concentrations of the analyses.

  • results: A list with the results of the analyses.

  • type: A character vector with the type of the analyses, which is "Statistic".

  • formats: A character vector with the file formats of the analyses, which is "csv".

Methods (by generic)

  • validate_object(StatisticAnalyses): Validate the StatisticAnalyses object, returns NULL if valid.

  • get_analysis_names(StatisticAnalyses): Get the names of the analyses, which is the row names of the analyses data frame.

  • get_analysis_classes(StatisticAnalyses): Get the classes assigned to each analysis.

  • set_analysis_classes(StatisticAnalyses): Set the classes of the analyses, where the argument value must be a character vector with the same length as the number of analyses.

  • get_concentrations(StatisticAnalyses): Get the concentration values of each analysis.

  • info(StatisticAnalyses): Get a data frame with the analyses, features, classes and concentrations.

  • add(StatisticAnalyses): Add new analyses to the StatisticAnalyses object, where the argument value must be a csv file or directly a data frame with the same column names as the existing analyses.

  • remove(StatisticAnalyses): Remove analyses from the StatisticAnalyses object, where the argument value can be a character vector with the names of the analyses or a numeric vector with the indices of the analyses to remove.

  • `[`(StatisticAnalyses) <- value: Add new analyses to the StatisticAnalyses object, where the argument value must be a csv file or directly a data frame with the same column names as the existing analyses.

  • `[[`(StatisticAnalyses) <- value: Add new analyses to the StatisticAnalyses object, where the argument value must be a csv file or directly a data frame with the same column names as the existing analyses.

  • plot_data(StatisticAnalyses): Plot the data of the StatisticAnalyses object.

Functions

  • set_concentrations(MassSpecAnalyses): Set the concentrations of the analyses, where the argument value must be a numeric vector with the same length as the number of analyses.