On Oct 25, 2011, at 10:40 AM, Assa Yeroslaviz wrote:

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

You just want to pass the start and end columns of genetable

> # Helper function
> inregion <- function(vec, locs) {
+ any( apply(locs, 1, function(x) vec["start"]>x[1] & vec["end"]<=x[2])) }
> # Test the function
> inregion(genetable[2, ], loctable[, c("Start", "End")])
[1] FALSE
> # [1] FALSE
>
> apply(genetable[, 3:4], 1, function(x) inregion(x, loctable[, c("Start", "End")]) )
[1] FALSE FALSE  TRUE FALSE FALSE

( I really wish that you would stop crossposting. I am only following your bad practice because you posted my code on BioC.)

--
David

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

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