plotSummaryProfile: plotSummaryProfile

In aCGH: Classes and functions for Array Comparative Genomic Hybridization data

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),
                   factor = 2.5, posThres=100, negThres=-0.75)

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
factor	factor specifies the number by which experimental variability should be multiples. Used only when tumor specific variability in aCGH.obj is not NULL. Defaults to 2.5
posThres	Threshold for gain. Set very high for homozygous deletion
negThres	Threshold for homozygous deletion

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)

aCGH documentation built on Nov. 8, 2020, 6:58 p.m.