[BioC] BayesPeak and RangedData obj output

Thu Nov 11 14:14:38 CET 2010

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 at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Binbin Liu [B.B.Liu at 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.

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