plotGainLoss {snapCGH} | R Documentation |
frequency plots and significance analysis
Description
The main application of this function is to plot the frequency of
changes.
Usage
plotGainLoss(segList, resT = NULL, pheno = rep(1,
ncol(log2ratios(segList))), chrominfo =
chrominfo.Mb, X = TRUE, Y = FALSE, rsp.uniq =
unique(pheno), all = length(rsp.uniq) == 1 &&
is.null(resT), titles = if (all) "All Samples" else
rsp.uniq, cutplot = 0, thres = 0.25, factor = 2.5, ylm
= c(-1, 1), p.thres = c(0.01, 0.05, 0.1), numaut = 22,
onepage = TRUE, colored = TRUE)
Arguments
segList |
Object of class SegList |
resT |
Data frame having the same structure as the result of
applying mt.maxT or mt.minP functions
from Bioconductor's multtest package for multiple testing.
The result is a data frame including the following 4 components:
'index', 'teststat', 'rawp' and 'adjp'.
|
pheno |
phenotype to compare. |
chrominfo |
Chromosomal information. Defaults to
chrominfo.Mb
|
X |
Include X chromosome? Defaults to yes. |
Y |
Include Y chromosome? Defaults to no. |
rsp.uniq |
rsp.uniq specified the codes for the groups of
interest. Default is the unique levels of the phenotype. Not used
when all is T.
|
all |
all specifies whether samples should be analyzed by subgroups
(T) or together (F).
|
titles |
titles names of the groups to be used. Default is the unique
levels of the pheno .
|
cutplot |
only clones with at least cutplot frequency of
gain and loss are plotted.
|
thres |
thres is either a vector providing unique
threshold for each sample or a vector of the same length as number
of samples (columns in data ) providing sample-specific
threshold. Used for plotting
the gain/loss frequency data as well as for clone screening and for
significance analysis when threshold is TRUE.Defaults to 0.25
|
factor |
factor specifies the number by which experimental
variability should be multiplied. Defaults to 2.5 |
ylm |
ylm vertical limits for the plot |
p.thres |
p.thres vector of p-value ciut-off to be plotted. computed
conservatively as the threshold corresponding to a given adjusted
p-value.
|
numaut |
numaut number of the autosomes |
onepage |
onepage whether all plots are to be plotted on one page or
different pages. When more than 2 groups are compared, we recommend multiple pages.
|
colored |
Is plotting in color or not? Default is TRUE. |
Examples
[Package
snapCGH version 1.0.0
Index]