BayesPeak and RangedData obj output
1
0
Entering edit mode
Binbin Liu ▴ 30
@binbin-liu-4350
Last seen 7.4 years ago
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.
BayesPeak BayesPeak • 698 views
0
Entering edit mode
@jonathan-cairns-4111
Last seen 7.4 years ago
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. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.