[BioC] PICS : makeRangedDataOutput

[Zhu, Lihua (Julie)]

Arnaud,

The makeRangedDataOutput outputs null when it should output a RangedData
object with peaks having score >=2. Here is the example you ran in Bioc2011
for ER dataset. Did I miss something? Thanks!

Best regards,

Julie

RD <- as(pics, "RangedData")
RD
RangedData with 304 rows and 1 value column across 2 spaces
           space               ranges   |     score
        <factor>            <IRanges>   | <numeric>
pics1      chr21 [42669615, 42669741]   |  98.27149
pics2      chr21 [42659913, 42660054]   |  88.79954
pics3      chr21 [41898880, 41899010]   |  85.83956
pics4      chr21 [45574708, 45574826]   |  81.39958
pics5      chr21 [45631173, 45631311]   |  79.91959
pics8      chr21 [15504544, 15504699]   |  59.93969
pics11     chr21 [42659615, 42659758]   |  46.61976
pics12     chr21 [15299644, 15299796]   |  46.12643
pics13     chr21 [39208579, 39208729]   |  43.65977
...          ...                  ... ...       ...
pics292    chr22 [33122494, 33122758]   |  1.874657
pics293    chr22 [43400868, 43401220]   |  1.849990
pics294    chr22 [38733327, 38733569]   |  1.553992
pics298    chr22 [14702383, 14702743]   |  1.479992
pics299    chr22 [17040892, 17041186]   |  1.479992
pics300    chr22 [22827324, 22827654]   |  1.479992
pics302    chr22 [15229177, 15229465]   |  1.331993
pics303    chr22 [15233278, 15233637]   |  1.257994
pics304    chr22 [15231777, 15232120]   |  1.109994

myFilter <- list(score=c(2, Inf), delta=c(50, 300), se=c(0,50))

RD <-makeRangedDataOutput(pics, type="bed", filter=myFilter)

RD
null

R version 2.14.0 beta (2011-10-17 r57293)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
base     

other attached packages:
 [1] ChipSeq_1.0.0        MotIV_1.7.0          rGADEM_2.1.0
seqLogo_1.19.0       BiocInstaller_1.1.28
 [6] snowfall_1.84        snow_0.3-7           PICS_1.7.0
BSgenome_1.21.7      Biostrings_2.21.11
[11] GenomicRanges_1.5.51 IRanges_1.11.31

loaded via a namespace (and not attached):
[1] lattice_0.19-33 tools_2.14.0