plotSummaryProfile: plotSummaryProfile

Description Usage Arguments Details See Also Examples

View source: R/aCGH.plotting.R

Description

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

Usage

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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

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data(colorectal)

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

Bioconductor-mirror/aCGH documentation built on June 1, 2017, 4:13 a.m.