summarize.clones {aCGH}R Documentation

Extracting summary information for all clones

Description

summarize.clones function is the text equivalent of plotFreqStat function - it summarizes the frequencies of changes for each clone accross tumors and when available assigns statistics. The resulting table can be easily exported.

Usage

summarize.clones(aCGH.obj, resT = NULL, pheno = rep(1, ncol(aCGH.obj)), rsp.uniq = unique(pheno), thres = 0.25, factor = 2.5, all = length(rsp.uniq) == 1 && is.null(resT), titles = if (all) "all" else rsp.uniq)

Arguments

aCGH.obj aCGH.obj object here
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'.Default is the unique levels of the phenotype. Not used when all is TRUE.
pheno phenotype to compare
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 TRUE.
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. If aCGH.obj has non-null sd.samples, then threshold is automatically replaced by tumor-specific sd multiplied by factor. Clone is considered to be gained if it is above the threshold and lost if it below negative threshold. Defaults to 0.25
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
all all specifies whether samples should be analyzed by subgroups (TRUE) or together (FALSE)
titles titles names of the groups to be used. Default is the unique levels of the pheno.

Value

Returns matrix containg the following information for each clones: annotation (same as in clones.info), number and proportion of samples where clone is present,gained and lost; and the same in each group if more than one group. Additionally, if significance comparison has been done, value of the statistic, unadjusted p-value and adjusted p-values are included for each clone.

Author(s)

Jane Fridlyand

See Also

plotFreqStat, aCGH

Examples

data(colorectal)
summarize.clones(colorectal)

[Package aCGH version 1.1.4 Index]