plotSummaryProfile {aCGH}R Documentation

plotSummaryProfile

Description

This function display the genomic events and tests for the differences between groups if they are specified.

Usage

plotSummaryProfile(aCGH.obj,
                   response = as.factor(rep("All", ncol(aCGH.obj))),
                   titles = unique(response[!is.na(response)]),
                   X = TRUE, Y = FALSE, maxChrom = 23,
                   chrominfo = human.chrom.info.Jul03,
                   num.plots.per.page = length(titles))

Arguments

aCGH.obj an object of aCGH class.
response phenotype to compare. defaults to all the samples being analyzed together.
titles titles for the groups, defaults to the name of the response
X logical indicating whether X needs to be shown
Y logical indicating whether Y needs to be shown
maxChrom this parameter controls how many chromosomes will be plotted, from 1 to maxChrom.
chrominfo a chromosomal information associated with the mapping of the data.
num.plots.per.page number of frequency plots per page. Default is the number of groups.

Details

This function utilizes output of the find.genomic.events by plotting it and testing between groups. The test are performed using kruskal-wallis rank test.

See Also

aCGH find.genomic.events

Examples


data(colorectal)

## Plotting summary of the sample profiles
plotSummaryProfile(colorectal)


[Package aCGH version 1.1.4 Index]