GeneSetTable-class {iSEEu}R Documentation

Gene set table

Description

A table where each row is a gene set and can be clicked to transmit a multiple feature selection to another panel. This has been deprecated in favor of the simpler FeatureSetTable.

Slot overview

The following slots control the type of gene sets to show:

The following slots control the table selections:

In addition, this class inherits all slots from its parent Panel class.

Constructor

GeneSetTable(...) creates an instance of a GeneSetTable class, where any slot and its value can be passed to ... as a named argument.

Supported methods

In the following code snippets, x is an instance of a GeneSetTable class. Refer to the documentation for each method for more details on the remaining arguments.

For defining the interface:

For monitoring reactive expressions:

For creating the table:

For controlling the multiple selections:

Author(s)

Aaron Lun

Examples

library(scRNAseq)
sce <- LunSpikeInData(location=FALSE)

library(scater)
sce <- logNormCounts(sce)

library(scran)
rowData(sce) <- cbind(rowData(sce), modelGeneVarWithSpikes(sce, "ERCC"))

# This defaults to 'org.Hs.eg.db' with 'ENTREZID'.
.setOrganism("org.Mm.eg.db")
.setIdentifierType("ENSEMBL")
gst <- GeneSetTable(PanelId=1L)

rdp <- RowDataPlot(RowSelectionSource="GeneSetTable1",
    ColorBy="Row selection",
    XAxis="Row data", XAxisRowData="mean", YAxis="total")

rdt <- RowDataTable(RowSelectionSource="GeneSetTable1")

if (interactive()) {
    iSEE(sce, initial=list(gst, rdp, rdt))
}


[Package iSEEu version 1.5.2 Index]