lcolladotor/derfinder — pull request #5 by mikelove (2013-11-14 19:17:10+00:00)
Title: import bumphunter, foldChange => log2FoldChange

note: I only passed check with --no-examples. otherwise I saw the following error:

pltCls> plotCluster(idx=1, regions=regsWithP$regions, annotation=annotation, coverageInfo=covInfo$coverage, groupInfo=group, txdb=TxDb.Hsapiens.UCSC.hg19.knownGene)
Error in initialize(value, ...) :
cannot use object of class “gg” in new(): class “Ideogram” does not extend that class
Calls: example ... plotIdeogram -> Ideogram -> new -> initialize -> initialize
In addition: Warning message:
In sampleDepth(list(genomeData$coverage), prob = 0.5, nonzero = TRUE, :
Sample column(s) 24, 25, 26, 28, 29, 30, 31 have sample depth coverage (nonzero=TRUE) as NA. Setting them to 0 (before centering if center=TRUE). Check for possible issues with this sample!
Calls: example ... source -> withVisible -> eval -> eval -> sampleDepth

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin12.5.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
[2] GenomicFeatures_1.14.0
[3] AnnotationDbi_1.24.0
[4] Biobase_2.22.0
[5] bumphunter_1.2.0
[6] locfit_1.5-9.1
[7] iterators_1.0.6
[8] foreach_1.4.1
[9] GenomicRanges_1.14.3
[10] XVector_0.2.0
[11] IRanges_1.20.5
[12] BiocGenerics_0.8.0
[13] derfinder_0.0.32
[14] RcppArmadillo_0.3.920.1
[15] Rcpp_0.10.6
[16] devtools_1.3
[17] BiocInstaller_1.12.0
[18] Defaults_1.1-1

loaded via a namespace (and not attached):
[1] biomaRt_2.18.0 Biostrings_2.30.1 biovizBase_1.10.3
[4] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4
[7] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7
[10] dichromat_2.0-0 digest_0.6.3 doRNG_1.5.5
[13] evaluate_0.5.1 ggbio_1.10.6 ggplot2_0.9.3.1
[16] grid_3.0.2 gridExtra_0.9.1 gtable_0.1.2
[19] Hmisc_3.12-2 httr_0.2 itertools_0.1-1
[22] labeling_0.2 lattice_0.20-24 MASS_7.3-29
[25] matrixStats_0.8.12 memoise_0.1 munsell_0.4.2
[28] pkgmaker_0.17.4 plyr_1.8 proto_0.3-10
[31] qvalue_1.36.0 R.methodsS3_1.5.2 RColorBrewer_1.0-5
[34] RCurl_1.95-4.1 registry_0.2 reshape2_1.2.2
[37] rngtools_1.2.3 rpart_4.1-3 Rsamtools_1.14.1
[40] RSQLite_0.11.4 rtracklayer_1.22.0 scales_0.2.3
[43] stats4_3.0.2 stringr_0.6.2 tcltk_3.0.2
[46] tools_3.0.2 VariantAnnotation_1.8.5 whisker_0.3-2
[49] XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.8.0