makeChrStrandData: Map a data matrix onto chromosome coordinates

In ChromHeatMap: Heat map plotting by genome coordinate

Description

Given an ExpressionSet, or a data matrix with row names corresponding to the probe or gene IDs in an accompanying annotation package, this function returns a data structure that can be used with the plotChrMap function. This code is based on the Makesense method from the geneplotter package, extended to use both the CHRLOC and CHRLOCEND annotation environments from recent AnnotationDbi packages.

In principle, any AnnotationDbi-based package could be used to provide chromosome location data to this function; all that matters is that the probe or gene identifiers used by the annotation package should be from the same source as the data ExpressionSet featureNames or matrix row names.

Usage

makeChrStrandData(expr, lib)

Arguments

expr	The ExpressionSet or data matrix to remap.
lib	The name of the annotation package to use.

Value

A ChrStrandData object suitable for use with plotChrMap.

Author(s)

Tim F Rayner

References

geneplotter, annotate and AnnotationDbi packages

See Also

plotChrMap, ChrStrandData-class

Examples

data('demo')
chrdata <- makeChrStrandData(exprs(ALLs.chr22), lib = "hgu95av2.db")

ChromHeatMap documentation built on Nov. 8, 2020, 7:33 p.m.