R version 3.0.1 Patched (2013-06-03 r62859) -- "Good Sport" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin12.3.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(bumphunter) Loading required package: IRanges 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 object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: GenomicRanges Loading required package: XVector Loading required package: foreach Loading required package: iterators Loading required package: locfit locfit 1.5-9.1 2013-03-22 Attaching package: ‘locfit’ The following object is masked from ‘package:GenomicRanges’: left, right > > ## Generate dummy data > set.seed(123) > dat <- dummyData() > > ## loessByCluster > loessSmoothed <- loessByCluster(cluster=dat$cluster, y=dat$mat[,1], + bpSpan = 1000, minNum=7, minInSpan=5, maxSpan=1) > save(loessSmoothed, file="../unitTests/loessSmoothed.rda") > > ## runmedByCluster > runmedSmoothed <- runmedByCluster(cluster=dat$cluster, y=dat$mat[,1], k=5, endrule="constant") > save(runmedSmoothed, file="../unitTests/runmedSmoothed.rda") > > ## bumphunter test 1 > set.seed(123) > bumpsTest1 <- bumphunter (dat$mat, design=dat$design, chr=dat$chr, pos=dat$pos, cluster=dat$cluster, + coef=2, cutoff=0.28, smooth=TRUE, B=500, + verbose=TRUE, smoothFunction=loessByCluster) bumphunterEngine: Using a single core (backend: doSEQ, version: 1.4.1) bumphunterEngine: Computing coefficients. bumphunterEngine: Smoothing coefficients. Loading required package: pkgmaker Loading required package: registry Attaching package: ‘pkgmaker’ The following object is masked from ‘package:IRanges’: new2 bumphunterEngine: Performing 500 permutations. bumphunterEngine: Computing marginal permutation p-values. bumphunterEngine: Smoothing permutation coefficients. bumphunterEngine: cutoff: 0.28 bumphunterEngine: Finding regions. bumphunterEngine: Computing regions for each permutation. bumphunterEngine: Estimating p-values and FWER. > save(bumpsTest1, file="../unitTests/bumpsTest1.rda") > > ## bumphunter test 2: chr unspecified > set.seed(123) > bumpsTest2 <- bumphunter (dat$mat, design=dat$design, pos=dat$pos, cluster=dat$cluster, + coef=2, cutoff=0.28, maxGap=500, smooth=TRUE, B=500, + verbose=TRUE, smoothFunction=loessByCluster) bumphunterEngine: Using a single core (backend: doSEQ, version: 1.4.1) bumphunterEngine: Computing coefficients. bumphunterEngine: Smoothing coefficients. bumphunterEngine: Performing 500 permutations. bumphunterEngine: Computing marginal permutation p-values. bumphunterEngine: Smoothing permutation coefficients. bumphunterEngine: cutoff: 0.28 bumphunterEngine: Finding regions. bumphunterEngine: Computing regions for each permutation. bumphunterEngine: Estimating p-values and FWER. > save(bumpsTest2, file="../unitTests/bumpsTest2.rda") > > > > proc.time() user system elapsed 9.171 0.123 9.283