summarize.clones: Extracting summary information for all clones
In aCGH: Classes and functions for Array Comparative Genomic Hybridization data

Description Usage Arguments Value Author(s) See Also Examples

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`	`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`.

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.

Jane Fridlyand

plotFreqStat, aCGH