Thanks for the clarification.
How do I filter the reads that occur exactly once?
________________________________
From: Martin Morgan
Cc: bioc-sig-sequencing@r-project.org
Sent: Wed, January 27, 2010 5:29:00 PM
Subject: Re: [Bioc-sig-seq] unique reads count
On 01/27/2010 02:57 PM, joseph wrote:
> If I understand this correctly, !duplicated does not count unique reads:
> !duplicated(c("A", "B", "B", "C"))
> [1] TRUE TRUE FALSE TRUE
>
> in your example, there are only two uniques (not 3 as counted by !duplicated).
Well, it depends on what your definition of 'duplicate' is, but yes, I
think we agree.
> Is it correct to say that the number of unique reads is given by the nReads when nOccurrences=1 using the tables function?
again unique needs definition (see unique(c("A", "B", "B", "C")), for
instance!) but yes, nOccurrences is the number of reads that occur
exactly once.
Martin
>
>
> ________________________________
> From: Martin Morgan
> Cc: bioc-sig-sequencing@r-project.org
> Sent: Wed, January 27, 2010 1:06:55 PM
> Subject: Re: [Bioc-sig-seq] unique reads count
>
> Hi Joseph --
>
> On 01/27/2010 12:33 PM, joseph wrote:
>> Hello
>> I have a ShortReadQ object:
>>> rfq
>> class: ShortReadQ
>> length: 16115723 reads; width: 34 cycles
>>
>> I used the negation of the result from srduplicated to count the unique reads:
>>> sum(!srduplicated(sread(rfq)))
>> [1] 4545719
>>
>> But also I looked at the frequency with which each read occurs using the tables function:
>>> head(tables(rfq_s_3_mel)$distribution)
>> nOccurrences nReads
>> 1 1 4022038
>> 2 2 255649
>
> srduplicated is behaving like 'duplicated', which is to return TRUE when
> an element has already been seen
>
>> duplicated(c("A", "B", "B", "C"))
> [1] FALSE FALSE TRUE FALSE
>
> There's one duplicate, the second 'B'.
>
> After example(srduplicated) I have
>
>> tables(sread(rfq))$distribution
> nOccurrences nReads
> 1 1 239
> 2 2 7
> 3 3 1
>> sum(srduplicated(sread(rfq)))
> [1] 9
>
> there are 7 reads that are the second of two reads, and 2 reads that are
> the second and third of three reads.
>
> Martin
>
>>
>> I expected that for nOccurrences=1, the nReads should be the same as what I got with !srduplicated.
>>
>> Can anybody explain why I got different counts?
>> Thank you
>> Joseph Dhahbi
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing@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
[[alternative HTML version deleted]]