[Bioc-sig-seq] about N statistics

Martin Morgan mtmorgan at fhcrc.org
Tue Sep 6 23:05:59 CEST 2011

On 09/06/2011 01:48 PM, wang peter wrote:
> thank you very much
> i think your answner is much more better


   tabulate(1L + nCount, wd)

which produces a vector of 0, 1, 2, ..., wd - 1 counts; this can be 
convenient if visiting several files, and wanting all to return a vector 
of length wd, eg., sapply() will then return a matrix that can be used 
in matplot() for visualization. '1L' is the same as as.integer(1).

Also, alphabetFrequency(sread(reads), baseOnly=TRUE)[,"other"] is more 
time- and memory-efficient (though maybe not enough to worry about) and 
works so long as 'N' means the same as "not 'A', 'C', 'G', 'T'".


> shan gao
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing

Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

More information about the Bioc-sig-sequencing mailing list