[BioC] tilingArray - plotAlongChrom problem

[Wolfgang Huber]

Dear Krys,

the plotAlongChrom function wants to plot data from both strands of a
strand-specific tiling array, such as shown here:
http://www.ebi.ac.uk/huber-srv/cgi-bin/viewYeastTilingArray.pl?gene=10:0555000

I have two answers, a disclaimer and then a technical reply:

1.) I understand your data is from a non-strand specific array (?). If
that is the case and you want to use the function, you'll need to tweak
it. We have tried to document the function properly, but it is doing a
lot of different things, pulls together data from different places, and
is not easy to use. Some effort in making it work on your own data
should be expected - hopefully still less than writing a similar
function from scratch. But I would recommend looking at the grid package
and consider 'plotAlongChrom' as a template from which you can work on,
rather than a ready-made product that will always work out of the box
for you.

Any concrete suggestions on where or how to improve the documentation
are welcome - remember that this is an 'open-source, open-development
project'.

2.) You didn't provide the output of "sessionInfo()". Please make sure
to use the latest version, e.g. by saying:

update.packages(repos='http://bioconductor.org/packages/1.9/bioc',
ask=FALSE)


I don't understand your code example, since you assign
  seg at x  <-array$Y/2
but then overwrite it
  seg at x <- as.vector(1:nrow(seg at y))

Possibly, to try the function, just adding
  assign("1.-", seg, segObj)
should work, then you'll see the same data twice in a layout as in the
example above.

Hope this helps, let me know if you have further questions (possibly we
can also discuss some in a visit of you at the EBI),

 Wolfgang



> I have data from a 650kb section of a chromosome on a tiling array. 
> 
> When I run a segmentation and try to plot the results along the chromosome I
> get the following error:
> 
>  > plotAlongChrom(segObj, chr=1, coord=c(1, 100000), gff=gff)
> Error in get(x, envir, mode, inherits) : variable "1.-.dat" was not found
> 
> Here is my code:
> 
> INFILE  <- "RH_i_vs_cell.txt"
> GFFFILE <- "t_gondii_ME49_Ib_650kb.gff"
> 
> array <- read.table(INFILE, header=TRUE)
> gff   <- read.table(GFFFILE, header=TRUE)
> 
> # maxseg corresponds to 50kb; longest gene in 650kb = 24,338bp (TASK data)
> maxseg <- 1000 
> maxk   <- 1000
> seg    <- segment(array$value, maxk=maxk, maxseg=maxseg)
> seg at x  <-array$Y/2 # add midpoints of probes to the segmentation object
> 
> # Do plotAlongChrom
> seg at x <- as.vector(1:nrow(seg at y))
> seg at flag <- rep(as.integer(0), times=12995)
> seg at nrSegments <- as.integer(111)
> 
> segObj <- new.env(parent=baseenv())
> assign("1.+", seg, segObj)
> 
> grid.newpage()
> plotAlongChrom(segObj, chr=1, coord=c(1, 100000), gff=gff)
> 
> I am finding the documentation in the R help and the "Segmentation demo"
> hard to follow and I would be grateful for any help about where I am going
> wrong.
> 
> Thanks
> 
> Krys
> 
> 
> Dr Krystyna A Kelly
> University of Cambridge
> Department of Pathology
> Molteno Building, Tennis Court Road
> Cambridge CB2 1QP
> Tel:    01223 333331
> Email: kak28 at cam.ac.uk
> 
> _______________________________________________
> 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


-- 
------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber