grabChrMapProbes: Identify the probes or genes plotted using plotChrMap

Description

Allows the user to interactively select regions of the plotChrMap heatmap, identifying all the probes or genes plotted in those regions.

Usage

grabChrMapProbes( plotmap )

Arguments

plotmap

The output of the plotChrMap function.

Value

A character vector of probe/gene identifiers. If multiple identifiers have been averaged into a single band these identifiers will be string concatenated, separated by semicolons. The start, end and interval arguments to plotChrMap can be used in such cases to plot the data at a higher resolution, splitting such loci into separate bands.

Details

This function takes the output of the plotChrMap function and uses it to identify the probes or genes responsible for the signals plotted on the plotChrMap heatmap. It asks the user to select two points on either side of the heatmap bands of interest (specifically, boundary for inclusion of a given band is its left-hand edge), and returns a vector of probe/gene identifiers. This can be passed directly to AnnotationDbi::mget to yield gene symbols and other annotation.

Note that the plotting area layout() and par() values are not reset on exit, so that this function can be reused as many times as is desired.

Examples

Run this code

data('demo')
plotmap <- plotChrMap(chrdata, '22', cytoband='q11.23')
probes <- grabChrMapProbes(plotmap)
library('hgu95av2.db')
genes <- mget(probes, hgu95av2SYMBOL, ifnotfound=NA)