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.
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)aCGH.obj object heremt.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.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 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 0.25factor specifies the number by which experimental variability should be multiples. used only when tumor specific variability in aCGH.obj is not NULL. Defaults to 2.5all specifies whether samples should be analyzed by subgroups (TRUE) or together (FALSE)titles names of the groups to be used. Default is the unique levels of the pheno.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.
plotFreqStat, aCGHdata(colorectal)
summarize.clones(colorectal)
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