[Bioc-sig-seq] Input from multiple Solexa runs

[Deepayan Sarkar]

On Thu, Apr 23, 2009 at 2:05 PM,  <ig2ar-saf2 at yahoo.co.uk> wrote:
>
> Thank you Deepayan.
>
> What package provides combineLaneReads()?

chipseq

>
> Ivan
>
>
>
>
>
> ----- Original Message ----
> From: Deepayan Sarkar <deepayan.sarkar at gmail.com>
> To: ig2ar-saf2 at yahoo.co.uk
> Cc: bioc-sig-sequencing at r-project.org
> Sent: Thursday, 23 April, 2009 16:37:57
> Subject: Re: [Bioc-sig-seq] Input from multiple Solexa runs
>
> On Thu, Apr 23, 2009 at 12:24 PM,  <ig2ar-saf2 at yahoo.co.uk> wrote:
>>
>> Hello,
>>
>> How do you pool together reads from multiple Solexa runs?
>>
>> Specificaly:
>>
>> Say that the structure of my hard drive looks like this
>>
>> /experiment01/GERALD_analysis01/(here all 8 lanes)
>> /experiment01/GERALD_analysis02/(here all 8 lanes)
>> /experiment02/GERALD_analysis01/(here all 8 lanes)
>>
>> Now say that my control1 lanes are in
>> experiment01, analysis01, lanes 1 and 2
>> experiment01, analysis02, lanes 3 and 4
>> (all four lanes are biologically identical)
>>
>> Now say that my treatment1 is in
>> experiment02, analysis01, lane 5 and 7
>>
>> Now say that I plan to read all Reads with a filter instance called myFilter.
>>
>> The question:
>>
>> How do I collect all that information into a single GenomeDataList object where I can call its GenomeData objects like this
>> myGenomeDataList$control1
>> myGenomeDataList$treatment1
>> ?
>>
>> Please try to answer the specific example because there is no alternative documentation.
>
> The function you are looking for is 'combineLaneReads'. If x is a
> GenomeDataList, then
>
> combineLaneReads(x)
>
> will give you a GenomeData object combining all reads in x.
> Additionally, you can treat a GenomeDataList object like a list, in
> the sense that you can subset them using [, combine them using c(),
> and changes their names using names()<-.
>
>
> So, let's say your per-run data are in variables called
>
> expt1_analysis1
> expt1_analysis2
> expt2_analysis1
>
> which are all GenomeDataList objects with names "1", "2", ..., "8" (I
> assume you know how to do this; as we discussed this a few days back).
> Then, the usage would be:
>
> control1 <- combineLaneReads(c(expt1_analysis1[c("1", "2")],
> expt1_analysis2[c("3", "4")]))
> treatment1 <- combineLaneReads(expt2_analysis1[c("5", "7")])
>
> (these would both be GenomeData objects). To combine them into a
> GenomeDataList, simply do
>
> myGenomeDataList <- GenomeDataList(list(control1 = control1,
> treatment1 = treatment1))
>
> or combining the two steps:
>
> myGenomeDataList <-
>    GenomeDataList(list(control1 =
> combineLaneReads(c(expt1_analysis1[c("1", "2")],
> expt1_analysis2[c("3", "4")])),
>                        treatment1 =
> combineLaneReads(expt2_analysis1[c("5", "7")])))
>
>
> -Deepayan
>
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