plotSegmentationSummary {snapCGH}R Documentation

plotSegmentationSummary

Description

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

Usage

plotSegmentationSummary(input, geList, response = as.factor(rep("All",
                 ncol(input))), titles =
                 unique(response[!is.na(response)]), X = TRUE, Y =
                 FALSE, maxChrom = 23, chrominfo = chrominfo.Mb,
                 num.plots.per.page = length(titles), factor = 2.5,
                 thresAbs = 100)

Arguments

input an object of either SegList or MAList class
geList an object of GEList 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 SegList is not NULL. Defaults to 2.5
thresAbs Threshold for gain. Set very high for homozygous deletion

Details

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

See Also

MAList findGenomicEvents


[Package snapCGH version 1.0.0 Index]