plotFeatures: Plot intensities of features.
In PAA: PAA (Protein Array Analyzer)

Description Usage Arguments Details Value Author(s) Examples

Plots intensities of all given features (one sub-plot per feature) in group- specific colors.

1 2	plotFeatures(features = NULL, elist = NULL, n1 = NULL, n2 = NULL, group1 = "group1", group2 = "group2", output.path = NULL)

`features`	vector containing `"BRC"`-IDs (mandatory).
`elist`	`EListRaw` or `EList` object containing all intensity data in log2 scale (mandatory).
`n1`	integer indicating the sample size of group 1 (mandatory).
`n2`	integer indicating the sample size of group 2 (mandatory).
`group1`	class label of group 1.
`group2`	class label of group 2.
`output.path`	string indicating the folder where the figure will be saved (optional).

Plots intensities of given features (e.g., selected by the function selectFeatures()) in group-specific colors (one sub-plot per feature). All sub-plots are aggregated to one figure. When the argument output.path is not NULL this figure will be saved in a tiff file in output.path. This function can be used to check whether the selected features are differential.

No value is returned.

Michael Turewicz, michael.turewicz@rub.de

cwd <- system.file(package="PAA")
load(paste(cwd, "/extdata/Alzheimer.RData", sep=""))
#elist <- elist[elist$genes$Block < 10,]

#c1 <- paste(rep("AD",20), 1:20, sep="")
#c2 <- paste(rep("NDC",20), 1:20, sep="")

#pre.sel.results <- preselect(elist=elist, columns1=c1, columns2=c2, label1="AD",
# label2="NDC", discard.threshold=0.1, fold.thresh=1.9, discard.features=TRUE,
# method="tTest")
#elist <- elist[-pre.sel.results$discard,]

#selectFeatures.results <- selectFeatures(elist,n1=20,n2=20,label1="AD",
# label2="NDC",selection.method="rf.rfe",preselection.method="none",subruns=2,
# k=2,candidate.number=20,method="frequency")

load(paste(cwd, "/extdata/selectFeaturesResultsFreq.RData", sep="")) 
plotFeatures(features=selectFeatures.results$features, elist=elist, n1=20,
 n2=20, group1="AD", group2="NDC")