plasma (version 1.1.4)

MultiOmics-class: Class "MultiOmics"

Description

The prepareMultiOmics function returns a new object of MultiOmics class for use in fitCoxModel.

Usage

prepareMultiOmics(datalist, outcome)
# S4 method for MultiOmics
summary(object, ...)
# S4 method for MultiOmics,missing
plot(x, y, ...)

Value

The prepareMultiOmics function returns a new object of the MultiOmics class.

Objects from the Class

Objects should be defined using the prepareMultiOmics constructor. In the simplest case, you enter two objects: a list of dataframes and a dataframe of clinical outcomes.

Arguments

datalist

a list of dataframes formatted to have variables as rows (dimension D) and samples as columns (dimension N).

outcome

a dataframe of clinical outcomes formatted to have sample names as row indexes and variable names as column indexes

object

An object of the MultiOmics class.

x

An object of the MultiOmics class.

y

Nothing; ignored.

...

Extra graphical or other parameters.

Slots

data:

A list of dataframes with variables as rows or varying length and samples as columns of uniform length N, where N is the maximum value of non-missing samples in any given dataset. Note that NAs have been added to “pad” to make the column length uniform across data types.

outcome:

A dataframe of clinical outcomes with variables as columns and samples as rows.

Methods

plot:

Produces a visual representation of the dimensionalities of each dataframe in datalist. D corresponds to the number of variables in each omics dataframe, and N corresponds to samples (or members) whose variable is not entirely missing. Gray areas correspond to missing samples.

summary:

Produces summary tables corresponding to datasets and outcomes.

Author

Kevin R. Coombes , Kyoko Yamaguchi

Examples

fls <- try(loadESCAdata())
if (inherits(fls, "try-error")) {
  stop("Unable to load data from remote server.")
}
MO <- with(plasmaEnv,
           prepareMultiOmics(datalist = assemble, outcome = Outcome))
plot(MO)
summary(MO)