[BioC] How to save the result from calling matchPWM?

[Hervé Pagès]

Hi Yisong,

Remember to search the 2 strands of the chromosome. The matchPWM
method for DNAString/MaskedDNAString/character objects does not
automatically do this for you. This is done with something like:

   plus_hits <- matchPWM(pwm, chr3R)
   minus_hits <- matchPWM(reverseComplement(pwm), chr3R)

You can save the hits as a tabulated file. For this you first
need to turn the 2 XStringViews object into a data.frame, which can
be done with something like:

   df <- rbind(data.frame(chrom="chr3R",
                          start=start(plus_hits), end=end(plus_hits),
                          strand="+"),
               data.frame(chrom="chr3R",
                          start=start(minus_hits), end=end(minus_hits),
                          strand="-"))

or, if you also want to save the hit sequences:

   df <- rbind(data.frame(chrom="chr3R",
                          start=start(plus_hits), end=end(plus_hits),
                          strand="+",
                          seq=as.character(plus_hits)),
               data.frame(chrom="chr3R",
                          start=start(minus_hits), end=end(minus_hits),
                          strand="-",
                          seq=as.character(minus_hits)))

(Note that this will report the hit sequences with respect to
the + strand, even for hits on the - strand. If you don't want
this, replace 'as.character(minus_hits)' above with
'as.character(reverseComplement(minus_hits))'.)

Then use something like write.table() to write 'df' to a file.

If you're looping over the chromosomes to find all the hits in the
genome, you can call write.table() with 'append=TRUE' to send all
the hits to the same file.

HTH,
H.


On 11/11/2013 11:36 PM, Yisong Zhen wrote:
> Dear Users,
>
> I called the matchPWM method in Biostrings package. The return object is
> XStringViews and I want to save the "hit" result in a file. It seemed that
> once there was a method named write.XStringViews, but I searched and found
> no corresponding information, maybe it already deprecated and
> not maintained any more. So, my question is, Is there any alternative way
> to save the result so that I can locate the motif hits in
> multiple sequences? Thanks in advance.
>
> Yisong
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319