GSNA (version 0.1.4.2)

gsnSubset: gsnSubset

Description

Create a subset GSNData object, containing only a subset of vertices or subnets.

Usage

gsnSubset(object, distance = NULL, vertex_names = c(), subnet_names = NULL)

Value

A new GSNData object is returned containing a subset of the vertices and subnets from the original GSNData object. For a given distance, the following data are subsetted for the included vertices and copied:

$distances[[distance]]$matrix

The raw distance matrix, subsetted.

$distances[[distance]]$pared

The pared distance matrix, subsetted.

$distances[[distance]]$edges

The edge list, subsetted

$distances[[distance]]$vertex_subnets

The vertex assignments for each subnet, subsetted.

$distances[[distance]]$clusters

The cluster assignments for each subnet, subsetted (for hierarchical clustering).

$distances[[distance]]$optimal_extreme

Character vector of length 1 indicating whether min or max distances are close in the raw distance matrix.

$distances[[distance]]$pared_optimal_extreme

Character vector of length 1 indicating whether min or max distances are close in the pared distance matrix.

The hclust object generated by hierarchical clustering is not currently subsetted or copied.

The default_distance is set as whichever distance matrix is copied. Currently, this function only supports copying a single distance matrix.

The following pathways data are copied:

$pathways$data

Pathways results, subsetted.

$pathways$type

The type of pathways results, copied.

$pathways$id_col

The identifier, copied.

$pathways$stat_col

Statistical column name, copied.

$pathways$sig_order

The significance order of the pathways results, based on the stat_column; are the pathways results to be sorted by significance from 'loToHi' (most significant values are low) or 'hiToLo' (most significant values high)?

Arguments

object

A GSNData object.

distance

Specifies a distance metric to use for subsetting. Defaults to the default_distance.

vertex_names

A character vector specifying the vertex names/gene sets to include in the GSNData subset object.

subnet_names

A character vector specifying the names of the subnets to include in the GSNData subset object.

Details

This function is useful for subsetting a single subnet, or a small set of subnets for the purpose of plotting just that subnet.

See Also

GSNData()