plotSummaryProfile {aCGH} | R Documentation |
This function display the genomic events and tests for the differences between groups if they are specified.
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)
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 |
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.
data(colorectal) ## Plotting summary of the sample profiles plotSummaryProfile(colorectal)