Extract: Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot'...

In markrobinsonuzh/iCOBRA: Comparison and Visualization of Ranking and Assignment Methods

Subsetting COBRAData, COBRAPerformance or COBRAPlot objects

Description

Functions to subset COBRAData, COBRAPerformance or COBRAPlot objects. COBRAData objects are subset by features (rows), while COBRAPerformance and COBRAPlot objects are subset by methods (columns). Numeric indices are not allowed, since not all slots may be arranged in the same order.

Usage

## S4 method for signature 'COBRAData'
x[i, j = "missing", drop = "missing"]

## S4 method for signature 'COBRAPerformance'
x[i = "missing", j, drop = "missing"]

## S4 method for signature 'COBRAPlot'
x[i = "missing", j, drop = "missing"]

Arguments

x	A COBRAData, COBRAPerformance or COBRAPlot object.
i	For COBRAData objects, a character vector of feature names to retain.
j	For COBRAPerformance and COBRAPlot objects, a character vector with method names to retain.
drop	not used.

Value

A subset of the original object, of the same class

Examples

data(cobradata_example)
cobradata_example[c("ENSG00000000457", "ENSG00000000971",
                    "ENSG00000000460"), ]
cobraperf <- calculate_performance(cobradata_example,
                                   binary_truth = "status",
                                   aspects = "fdrtpr")
cobraperf[, c("voom")]
cobraplot <- prepare_data_for_plot(cobraperf)
cobraplot[, c("voom")]

markrobinsonuzh/iCOBRA documentation built on Nov. 7, 2024, 7:11 a.m.