Hi, We've noticed that using runmean on Rles with all elements being a mix of positive or zero numbers sometimes results in some very small negative numbers. Is it possible for it to be exactly zero ?
> cvg 'numeric' Rle of length 199432144 with 1495580 runs Lengths: 35100 35 ... 18 Values : 0 0.750447078847223 ... 0.750447078847223 > negs <- which(cvg < 0) > negs integer(0) > smCvg <- IRanges::runmean(cvg, 1001, endrule = "constant") > negs <- which(smCvg < 0) > smCvg[head(negs)] 'numeric' Rle of length 6 with 1 run Lengths: 6 Values : -1.56163238628593e-16 > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7 [3] affxparser_1.22.0 R.huge_0.2.0 [5] aroma.core_1.7.0 aroma.light_1.18.0 [7] matrixStats_0.2.2 R.rsp_0.4.0 [9] R.cache_0.3.0 R.filesets_0.9.0 [11] digest_0.4.2 R.utils_1.5.3 [13] R.oo_1.7.4 R.methodsS3_1.2.1 [15] BSgenome.Hsapiens.UCSC.hg18_1.3.16 BSgenome_1.18.3 [17] Biostrings_2.18.2 GenomicRanges_1.2.3 [19] IRanges_1.8.9 loaded via a namespace (and not attached): [1] Biobase_2.10.0 tools_2.12.0 -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
