msarc (version 1.3.2)

msarc.plotHeatmap: Correlation Heat Maps for Mass Spec Experiments

Description

Given 3 or more mass spec experiments as msarc objects, this function draws a heat map of the similarity among the experiments. Similarity may be calculated based on similarity of scores, or simply by the presence or absence of individual UniProt accession id's.

Usage

msarc.plotHeatmap(msalist, method = "euclidean", useScore = T, ...)

Arguments

msalist

a list of msarc objects.

method

Correlation method to pass to dist. Acceptable values are whatever dist supports, currently "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". See the docume

useScore

If true (the default), use the score of each peptide in computing the correlation. If false, just use the presence or absence of each protein in each experiment.

...

Other parameters to pass to heatmap.2 from package gplots.

Value

• the distance matrix calculated by dist.

Details

The samples must have distinct filenames, or this function will fail. You can load the samples from mass spec files, or just explicitly set object$filename for each msarc object. These filenames will also be used as labels in the heat map.

References

Gregory R. Warnes. Includes R source code and/or documentation contributed by: Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz and Bill Venables (2011). gplots: Various R programming tools for plotting data. R package version 2.10.1. http://CRAN.R-project.org/package=gplots

See Also

See also heatmap.2 from package gplots and dist from package stats.

Examples

data('sample_cluster',package="msarc")
msarc.plotHeatmap(sample_cluster)