PAA (version 1.7.1)

plotFeatures: Plot intensities of features.

Description

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

Usage

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

Arguments

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).

Value

No value is returned.

Details

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.

Examples

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")