[Bioc-sig-seq] coverage vectors and subseq

[kirti prakash]

Hi Martin,

Thanks a lot for your help. Bioconductor is a great place as one gets
the help from the best and its completely free. Its seems all one
needs to do good research in bioinformatics is a computer, some data
and Bioconductor.

Its the same tutorial... the link you mentioned above . I cannot
attach the tutorials due to the limit of mail size.

I did exactly as you told and most the things work fine except...

Later in the tutorial they use deltaConvolve function...

H3K4me1 <- deltaConvolve( cov.H3K4me1.chr10, tss, martReply$strand ==
-1, left=win[1], right=win[2] )
Error in .bracket.Index(i, lx, asRanges = TRUE) :
 range index out of bounds
Error in as.vector(seqselect(coverage, winCentres[i] + left, winCentres[i] +  :
 error in evaluating the argument 'x' in selecting a method for
function 'as.vector'

Also you mention endoapply above... it also gave me same error...

endoapply(cov.H3K4me1, seqselect, 123456-50, 123456+50)
Error in .bracket.Index(i, lx, asRanges = TRUE) :
 range index out of bounds


I found that both of these are exception handling errors but I again I
don't know to fix them. It would be great if you can again help on
this.

Thanks again,

Best Regards,

Kirti Prakash

On Wed, Aug 18, 2010 at 7:33 AM, kirti prakash
<kirtiprakash3.14 at gmail.com> wrote:
> Hi Martin,
>
> Thanks a lot for your help. Bioconductor is a great place as one gets
> the help from the best and its completely free. Its seems all one
> needs to do good research in bioinformatics is a computer, some data
> and Bioconductor.
>
> Its the same tutorial the link you mentioned above . In future I will
> attach the pdfs of the tutorials also.
>
> I did exactly as you told and most the things work fine except...
>
> Later in the tutorial they use deltaConvolve function...
>
> H3K4me1 <- deltaConvolve( cov.H3K4me1.chr10, tss, martReply$strand ==
> -1, left=win[1], right=win[2] )
> Error in .bracket.Index(i, lx, asRanges = TRUE) :
>  range index out of bounds
> Error in as.vector(seqselect(coverage, winCentres[i] + left, winCentres[i] +  :
>  error in evaluating the argument 'x' in selecting a method for
> function 'as.vector'
>
> Also you mention endoapply above... it also gave me same error...
>
> endoapply(cov.H3K4me1, seqselect, 123456-50, 123456+50)
> Error in .bracket.Index(i, lx, asRanges = TRUE) :
>  range index out of bounds
>
>
> I found that both of these are exception handling errors but I again I
> don't know to fix them. It would be great if you can again help on
> this.
>
> Thanks again,
>
> Best Regards,
>
> Kirti Prakash
>
>
>
>
> On Tue, Aug 17, 2010 at 7:47 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>> kirti prakash <kirtiprakash3.14 at gmail.com> writes:
>>
>>> Hi,
>>>
>>> I was reading the material "EMBL course on Short Read analysis with
>>> Bioconductor: An exercise with coverage vectors" by Simon Anders.
>>
>> It took me a second to find
>>
>>  http://bioconductor.org/help/course-materials/2009/EMBLJune09/Practicals/TSS/
>>
>> is that the tutorial you mean?
>>
>>>
>>> I tried this...
>>> aln <- readAligned("dirPath", pattern="sequence.map", type="Bowtie")
>>> cov = coverage(aln)
>>> cov
>>> [[1]]
>>> SimpleRleList of length 25
>>> $chr1
>>> 'integer' Rle of length 247188620 with 840106 runs
>>>  Lengths:    463     36   6823     36 550058 ...    713     36   2034     36
>>>  Values :      0      1      0      1      0 ...      0      1      0      2
>>>
>>> $chr10
>>> 'integer' Rle of length 135373320 with 446681 runs
>>>  Lengths: 88078    36  3880    36 12451 ...    20    50    36 22054    36
>>>  Values :     0     1     0     1     0 ...     1     0     1     0     1
>>> .
>>> .
>>> .
>>>
>>>>cvg <- cov$chr10
>>>> as.vector(subseq(cvg, 123456+50, 123456-50))
>>
>> I think this should be
>>
>>  seqselect(cvg$chr10, 123456+50, 123456-50)
>>
>> or, to subset all chromosomes,
>>
>>  endoapply(cvg, seqselect, 123456+50, 123456-50)
>>
>> (though it doesn't seem like you'd usually want to select consistent
>> coordinates across chromosomes).
>>
>> To get here, I looked up the help page for Rle-class
>>
>>  > class?Rle
>>
>> This is with
>>
>>> sessionInfo()
>> R version 2.11.1 Patched (2010-06-03 r52215)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>  [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>>  attached base packages:
>>  [1] stats     graphics  grDevices utils     datasets  methods
>>  base
>>
>>  other attached packages:
>>  [1] ShortRead_1.6.2     Rsamtools_1.0.5     lattice_0.18-8
>>  [4] Biostrings_2.16.9   GenomicRanges_1.0.5 IRanges_1.6.11
>>
>>  loaded via a namespace (and not attached):
>>  [1] Biobase_2.8.0 grid_2.11.1   hwriter_1.2   tools_2.11.1
>>
>> Martin
>>
>>
>>> Error in function (classes, fdef, mtable)  :
>>>  unable to find an inherited method for function "subseq", for signature "list"
>>> Error in as.vector(subseq(cvg, 123456 + 50, 123456 - 50)) :
>>>  error in evaluating the argument 'x' in selecting a method for
>>> function 'as.vector'
>>>
>>> I guess * 'integer' Rle of length* should be 'numeric' Rle of length
>>> as per the booklet ... but I don't know how to fix it.
>>>
>>> I know I am making some stupid mistake. It would be great if anyone
>>> can provide some help on this.
>>>
>>> Thank you,
>>>
>>> Best regards,
>>>
>>> Kirti Prakash
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>>
>