Henrik:
The help() function is what i am looking for!
Thanks,
Yupu
On Oct 21, 3:05 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> Hi.
>
> On Tue, Oct 21, 2008 at 8:48 AM, yupu <[EMAIL PROTECTED]> wrote:
>
> > Henrik:
>
> > Hi, thanks for the response!
>
> > Is there any way for me to find out all available APIs ( or functions)
> > that come with the package?
>
> > I tried ?getUnitsOnChromosome but there is not much information
> > there :-S
>
> I don't have the time to write detailed Rd help pages for end users
> (and keep them up to date, which is the time-consuming part). I do
> not know how many functions and methods there are, but we're talking
> about more than 1000 pages of code. However, you can trust that the
> usage/synopsis and the arguments are correct for Rd files. The Rd
> help for a lot of the methods/functions are directed to a common page
> (explaining it is still to be documented). The ones that exists are
> mostly intended for developers, but developers tend to look at/follow
> the source code instead.
>
> Instead, my strategy is to document the package online. Some features
> are also revealed in replies on the mailing list itself - so it's
> worth skimming through message from others too. When a feature
> discussed in the forum becomes frequently used, I try to write up a
> page or add it to a vignette.
> What is there you can trust. I am very conservative about what parts
> of the API I make "public" this way, because for each new
> method/feature I expose I will also have to keep backward compatible
> which takes time.
>
> The design of classes in aroma.affymetrix can be though of as classic
> object-oriented programming as seem in C++, Java etc. This means that
> you have an object of a certain class and there exist methods coupled
> to that class. If you know the class, you can quickly get a list of
> methods available, e.g.
>
> > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6")
> > class(cdf)[1]
>
> [1] "AffymetrixCdfFile"
> # The Rd files for classes show an automatically generated list of all
> (non-private) methods.> help(AffymetrixCdfFile)
>
> # You can get the same list by> AffymetrixCdfFile
>
> AffymetrixCdfFile extends UnitNamesFile, AromaChipTypeAnnotationFile,
> Affymetrix
> File, AromaPlatformInterface, AromaMicroarrayDataFile, GenericDataFile,
> Object {
> public convert(chipType=getChipType(this), suffix=NULL, sep="-",
> path="cdf", .
> .., verbose=FALSE)
> public createMonoCell(...)
> public getCellIndices(units=NULL, ..., useNames=TRUE, unlist=FALSE,
> force=FALS
> E, cache=TRUE, verbose=FALSE)
> public getChipType(fullname=TRUE, ...)
> public getDimension(...)
> ...[snip]
>
> That may or not may be useful for advanced users.
>
> As you work with the packages and maybe look at/follow the code
> occasionally, you well learn the overall structure, design and sprit
> of the package, which I hope will help out too. Posting questions
> like yours is also a good for finding out about non-documented
> features. If I see there are common use cases, I will not only try to
> add methods to simplify them, but also document them online.
>
> Conclusion: Use the aroma.affymetrix webpage/forum for documentation/help.
>
> /Henrik
>
>
>
> > Thanks!
> > Yupu
>
> > On Oct 20, 8:12 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> >> Forgot one thing below:
>
> >> On Mon, Oct 20, 2008 at 5:02 PM, Henrik Bengtsson <[EMAIL PROTECTED]>
> >> wrote:
> >> > Hi,
>
> >> > On Mon, Oct 20, 2008 at 3:51 PM, yupu <[EMAIL PROTECTED]> wrote:
>
> >> >> Hi,
>
> >> >> I am using aroma.affymetrix to do copy number estimation on
> >> >> affymetrix's SNP6.0 data.
>
> >> >> I followed the instructions from
> >> >>http://groups.google.com/group/aroma-affymetrix/web/total-copy-number...
>
> >> >> Things went smoothly, untill I realized there is no data point for at
> >> >> position 51598 on Chr1 that is corresponding to probe id CN_473963.
>
> >> >>>units <- getUnitsOnChromosome(gi,chromosome=1)
> >> >>>pos<- getPositions(gi,units=units)
> >> >>>bool <- pos == 51598
> >> >>> pos[bool]
> >> >> integer(0)
>
> >> >> Did I do anything wrong? Or aroma is now dealing with these probes yet
> >> >> for the moment?
>
> >> > Don't rely on exact genomic position in order to identify/refer to a
> >> > CN variant/probe, because this information tend to get updated
> >> > whenever the human genome annotation data is updated. Doing that is
> >> > also error prone to differences in how positions are defined, e.g. if
> >> > the first position of a chromsome is 0 or 1 (which might be issue in
> >> > this case).
>
> >> > Instead, use the unit name to identify the position and not the other
> >> > way around, e.g.
>
> >> >> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> >> >> gi <- getGenomeInformation(cdf);
> >> >> unit <- indexOf(cdf, name="CN_473963");
> >> >> unit
> >> > [1] 935591
> >> >> pos <- getPositions(gi, units=unit);
> >> >> pos
> >> > [1] 51599
>
> >> > If you really want to identify a unit name given a position, allow for
> >> > some shift, say +/-5 nucleotides, e.g.
>
> >> >> units <- getUnitsOnChromosome(gi, chromosome=1);
> >> >> pos <- getPositions(gi, units=units);
> >> >> idxs <- which(51598-5 <= pos & pos <= 51598+5);
> >> >> units[idxs];
> >> > [1] 935591
> >> >> pos[idxs];
> >> > [1] 51599
>
> >> A better way to identify units in a specific region on a given chromosome
> >> is:
>
> >> > units <- getUnitsOnChromosome(gi, chromosome=1, region=c(51598-5,
> >> > 51598+5));
> >> > units
> >> [1] 935591
> >> > pos <- getPositions(gi, units=units);
> >> > pos
> >> > [1] 51599
>
> >> I forgot about the 'region' arguments.
>
> >> /Henrik
>
> >> > Cheers
>
> >> > /Henrik
>
> >> >> Thanks,
> >> >> Yupu
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