[Bioc-sig-seq] Operations between sets of ChIP-seq peak locations

[Ivan Gregoretti]

Thank you.

Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878



On Thu, Jan 28, 2010 at 1:46 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> A[!ranges(A) %in% ranges(B),]
>
> On Thu, Jan 28, 2010 at 7:46 AM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
>>
>> Hi everybody,
>>
>> I have two sets of ChIP-seq peaks: A and B.
>> How do I select the peaks in A that are not overlapped by any peak in B?
>>
>>
>> Now in more detail:
>>
>> I do
>>
>> library(rtracklayer)
>> A <- import('condition_A.bed', 'bed')
>> B <- import('condition_B.bed', 'bed')
>>
>> they are both RangedData instances.
>>
>> I need to compute A - B.
>>
>> How do you guys do it?
>>
>> Thank you,
>>
>> Ivan
>>
>>
>> Ivan Gregoretti, PhD
>> National Institute of Diabetes and Digestive and Kidney Diseases
>> National Institutes of Health
>> 5 Memorial Dr, Building 5, Room 205.
>> Bethesda, MD 20892. USA.
>> Phone: 1-301-496-1592
>> Fax: 1-301-496-9878
>>
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>
>