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]