Hi all,
@Martin - thanks for the help it works very good.
@David - sorry for the misunderstanding. I will see to it, that it won't
happen again.
BTW, unfortunately your function is not working.
It is patialy my error as I gave no regions with overlaps, but even after
changing them it just doesn't fit.
Here is the new data with an overlap in the third gene:
genetable <- rd.txt("name chr start end str
accession Length
gen1 4 646752 646838 + MI0005806 86
gen12 2L 243035 243141 - MI0005821 106
gen3 2L 159838 159928 + MI0005813 90
gen7 2L 1831685 1831799 - MI0011290 114
gen4 2L 2737568 2737661 + MI0017696 93")
loctable <- rd.txt("Chr Start End length
4 136532 138654 2122
3 139870 141970 2100
2L 157838 160440 2602
X 160834 162966 2132
4 204040 208536 4496")
But I still get:
> apply(genetable, 1, function(x) inregion(x, loctable[, c("Start",
"End")]) )
[1] FALSE FALSE FALSE FALSE FALSE
for the single queries I get TRUE:
> inregion(genetable[3, ], loctable[, c("Start", "End")])
[1] TRUE
Do you have Idea, as to how I can fix this problem?
Thanks and again sorry for the trouble.
Assa
On Tue, Oct 25, 2011 at 15:48, Martin Morgan <mtmor...@fhcrc.org> wrote:
> On 10/25/2011 03:42 AM, Assa Yeroslaviz wrote:
>
>> Hi everybody,
>>
>> I would like to know whether it is possible to compare to tables for
>> certain
>> parameters.
>> I have these two tables:
>> gene table
>> name chr start end str accession Length
>> gen1 4 646752 646838 + MI0005806 86
>> gen12 2L 243035 243141 - MI0005821 106
>> gen3 2L 159838 159928 + MI0005813 90
>> gen7 2L 1831685 1831799 - MI0011290 114
>> gen4 2L 2737568 2737661 + MI0017696 93
>> ...
>>
>> localization table:
>> Chr Start End length
>> 4 136532 138654 2122
>> 3 139870 141970 2100
>> 2L 157838 158440 602
>> X 160834 162966 2132
>> 4 204040 208536 4496
>> ...
>>
>> I would like to check whether a specific gene lie within a certain region.
>> For example I want to see if gene 3 on chromosome 2L lies within the
>> region
>> given in the second table.
>>
>
> Hi Assa --
>
> In Bioconductor, use the GenomicRanges package. Create two GRanges objects
>
> genes = with(genetable, GRanges(chr, IRanges(start, end), str,
> accession=accession, Length=length)
> locations = with(locationtable, GRanges(Chr, IRanges(Start, End)))
>
> then
>
> olaps = findOverlaps(genes, locations)
>
> queryHits(olaps) and subjectHits(olaps) index each gene with all locations
> it overlaps. The definition of 'overlap' is flexible, see ?findOverlaps.
>
> Martin
>
>
>
>> What I would like to is like
>> 1. check if the gene lies on a specific chromosome
>> 1.a if no - go to the next line
>> 1.b if yes - go to 2
>> 2. check if the start position of the gene is bigger than the start
>> position
>> of the localization table AND if it smaller than the end position (if it
>> lies between the start and end positions in the localization table)
>> 2.a if no - go to the next gene
>> 2.b if yes - give it to me.
>>
>> I was having difficulties doing it without running into three interleaved
>> conditional loops (if).
>>
>> I would appreciate any help.
>>
>> Thanks
>>
>> Assa
>>
>> [[alternative HTML version deleted]]
>>
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>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>
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