SVTable-class: Summary-Variation Table

In sbcblab/geva: Gene Expression Variation Analysis (GEVA)

Description

The SVTable class stores a matrix composed by two columns: S (for summary) and V (for variation).

This class is inherited by GEVASummary.

Value

A SVTable object

Slots

sv

matrix composed by two columns: S (summary) and V (variation)

Methods

Alternative accessors

summary(object, ...)

Returns the S column

sv.data(object)

Equivalent to returning this object itself

variation(object, ...)

Returns the V column

Constructor

svtable(S, V, row.names = NULL)

Creates a SVTable from the vectors S and V

Conversion and coercion

as.data.frame(x, ...)

Converts this object to data.frame

as.matrix(x, ...)

Converts this object to matrix

as.SVTable.data.frame(x, row.names = rownames(x), ...)

Converts a data.frame to a SVTable

as.SVTable.matrix(x, row.names = rownames(x), ...)

Converts a matrix to a SVTable

as.SVTable(x, ...)

Returns the same object

Dimension accessors

dimnames(x)

Gets a list with the row and column names from the sv slot.
Individual dimension names can also be accessed through rownames and colnames

dim(x)

Gets the dimensions from the sv slot

length(x)

Returns the number of rows in the sv slot

names(x)

Always returns c('S', 'V')

Formatting and evaluation

format(x, ...)

Generic format implementation for SVTable

with(data, expr, ...)

Generic with implementation for SVTable

Plotting

plot(x, y, ...)

Draws a SV-plot. The horizontal axis is for summary (S) and the vertical axis is for variation (V)

points(x, ...)

Draws the SV points in the plot

Subsetting

head(x, n = 6L, ...)

Returns the first parts of the matrix contents

tail(x, n = 6L, ...)

Returns the last parts of the matrix contents

Validation

is.na(x)

Generic is.na implementation for SVTable

Note

The matrix from sv slot can be numeric, character, or any other supported type by matrix. The same slot from GEVASummary, however, is always a numeric matrix.

Examples

## Creates a SV-table where:
# - S has elements from 1 to 10; and
# - V has elements from 10 to 1
svtab <- svtable(seq.int(1, 10), seq.int(10, 1))

sbcblab/geva documentation built on March 15, 2021, 10:08 p.m.