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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