[BioC] BayesPeak and RangedData obj output

[Binbin Liu]

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.