Hello there, I have two questions here to ask for your suggestions regarding BayesPeak pkg and RangedData obj output. I am trying to use BayesPeak for peak identification of my treat with input After done: raw.chr1 = bayespeak(treat, control, chr="chr1", use.multicore=T, mc.cores=16) output.chr1 = summarize.peaks(raw.chr1, method="lowerbound") I had a look at peaks in output.chr1 ---- RangedData with 1376 rows and 1 value column across 1 space space ranges | PP <character> <iranges> | <numeric> 1 chr1 [33146139, 33146289] | 0.9333376 2 chr1 [33381689, 33381839] | 0.9753039 3 chr1 [33382089, 33382289] | 0.9999574 4 chr1 [33504139, 33504289] | 0.9997761 5 chr1 [33561739, 33561939] | 0.9999883 6 chr1 [33563589, 33563839] | 1.0000000 7 chr1 [33622739, 33622939] | 0.9999843 8 chr1 [33627989, 33628139] | 0.9997822 9 chr1 [33644589, 33644939] | 0.9999988 10 chr1 [33646539, 33646689] | 0.9771097 and attributes(output.chr1) ---- attributes(outputchr1) $ranges CompressedIRangesList of length 1 $chr1 IRanges of length 1376 start end width [1] 33146139 33146289 151 [2] 33381689 33381839 151 [3] 33382089 33382289 201 [4] 33504139 33504289 151 [5] 33561739 33561939 201 [6] 33563589 33563839 251 [7] 33622739 33622939 201 [8] 33627989 33628139 151 [9] 33644589 33644939 351 ... ... ... Does this look normal to you?, because I am not sure. It seems that all peaks have very similar width and coordinates. I have tried with different chip-seq dataset and got similar pattern of output as this. What have I done wrong here? The second question is when I try to write output with write.table(output.chr1, file="blah.txt", sep="\t") as shown on the BayesPeak tutorial, R complains that "Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class structure("RangedData", package = "IRanges") into a data.frame" What is wrong here? sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] multicore_0.1-4 BayesPeak_1.2.0 IRanges_1.4.16 loaded via a namespace (and not attached): [1] tools_2.10.1 Many thanks for any help.

Dear Binbin, This behaviour is correct - BayesPeak divides the chromosome into 100bp bins (by default). Because we perform an additional offset analysis, this is refined to 50bp resolution. This number is usually much smaller than peak widths and so is sufficient for most purposes. Are you using the tutorial "ChIP-seq practical: peak detection and peak annotation"? This document was written a year ago, and BayesPeak has evolved quite a bit since then. I would strongly recommend using the current vignette instead (opened with the R command vignette("BayesPeak")). The function export() in the rtracklayer library may be of use for the task you are interested in performing. In particular, sections 7 and 8 in the vignette are worth reading, as it may be necessary to apply an overfitting correction. Thanks, Jonathan ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Binbin Liu [B.B.Liu@leeds.ac.uk] Sent: 11 November 2010 12:17 To: bioconductor at stat.math.ethz.ch Subject: [BioC] BayesPeak and RangedData obj output Hello there, I have two questions here to ask for your suggestions regarding BayesPeak pkg and RangedData obj output. I am trying to use BayesPeak for peak identification of my treat with input After done: raw.chr1 = bayespeak(treat, control, chr="chr1", use.multicore=T, mc.cores=16) output.chr1 = summarize.peaks(raw.chr1, method="lowerbound") I had a look at peaks in output.chr1 ---- RangedData with 1376 rows and 1 value column across 1 space space ranges | PP <character> <iranges> | <numeric> 1 chr1 [33146139, 33146289] | 0.9333376 2 chr1 [33381689, 33381839] | 0.9753039 3 chr1 [33382089, 33382289] | 0.9999574 4 chr1 [33504139, 33504289] | 0.9997761 5 chr1 [33561739, 33561939] | 0.9999883 6 chr1 [33563589, 33563839] | 1.0000000 7 chr1 [33622739, 33622939] | 0.9999843 8 chr1 [33627989, 33628139] | 0.9997822 9 chr1 [33644589, 33644939] | 0.9999988 10 chr1 [33646539, 33646689] | 0.9771097 and attributes(output.chr1) ---- attributes(outputchr1) $ranges CompressedIRangesList of length 1 $chr1 IRanges of length 1376 start end width [1] 33146139 33146289 151 [2] 33381689 33381839 151 [3] 33382089 33382289 201 [4] 33504139 33504289 151 [5] 33561739 33561939 201 [6] 33563589 33563839 251 [7] 33622739 33622939 201 [8] 33627989 33628139 151 [9] 33644589 33644939 351 ... ... ... Does this look normal to you?, because I am not sure. It seems that all peaks have very similar width and coordinates. I have tried with different chip-seq dataset and got similar pattern of output as this. What have I done wrong here? The second question is when I try to write output with write.table(output.chr1, file="blah.txt", sep="\t") as shown on the BayesPeak tutorial, R complains that "Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class structure("RangedData", package = "IRanges") into a data.frame" What is wrong here? sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] multicore_0.1-4 BayesPeak_1.2.0 IRanges_1.4.16 loaded via a namespace (and not attached): [1] tools_2.10.1 Many thanks for any help. _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor This communication is from Cancer Research UK. 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