A wrapper function to run existing breakpoint detection algorithms on arrayCGH data. Currently only DNAcopy is implemented.
Object of class
Boundary for short vs long segments, in number of features
Relative undo sd for long segments. See details.
The method to be used for breakpoint detection. Currently only DNAcopy is supported, which will run the
segment for details on the algorithm. About
these are only relevant when
sdundo is set, in combination with
relSDlong provides the undo sd for long segments, which equals
undo.SD is then used for short segments.
In the example below, short segments are considered to contain
less or equal to
clen=10 features. The example below undoes splits for two consecutive short segments if these are less than
undo.SD=3 sd apart,
while it undoes splits for two long segments if these are less than
undo.SD/relSDlong=3/3=1 sd apart. If, for two consecutive segements, one is short and one is long,
splits are undone in the same way as for two short segments.
This function returns a dataframe in the same format as the input with segmented arrayCGH data.
Sjoerd Vosse & Mark van de Wiel
Venkatraman, A.S., Olshen, A.B. (2007). A faster circulary binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 23, 657-663.
data(WiltingNorm) ## Not run: segmented.data <- segmentData(WiltingNorm, alpha=0.02,clen=10,relSDlong=3,undo.SD=3,undo.splits="sdundo")
Loading required package: impute Loading required package: DNAcopy Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: CGHbase Loading required package: marray Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Loading required package: snowfall Loading required package: snow Attaching package: 'snow' The following objects are masked from 'package:BiocGenerics': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, parApply, parCapply, parLapply, parRapply, parSapply The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, makeCluster, parApply, parCapply, parLapply, parRapply, parSapply, splitIndices, stopCluster Attaching package: 'CGHcall' The following object is masked from 'package:BiocGenerics': normalize
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