makeChrStrandData

The ExpressionSet or data matrix to remap.

expr

The name of the annotation package to use.

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 <code>plotChrMap</code>
 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.

array

The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.

Tim F Rayner

ChromHeatMap

Heat map plotting by genome coordinate

makeChrStrandData function

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 <code>plotChrMap</code>
 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.

makeChrStrandData: Map a data matrix onto chromosome coordinates

Description

Usage

Arguments

Value

References

See Also

Examples