[BioC] Query regarding accessing all genes within a BAC

[Steffen Durinck]

Dear Rifat,

No this is not possible. One way to do it is if you can map the BAC's to 
chromosome, start and end positions on the chromosome and then look up 
the genes using the getFeature function. For PAC14E10 that would give:

 > mart<-martConnect()
 > getFeature(chromosome=1, start=981787, end=1204439, 
type="hugo",mart=mart, species="hsapiens")
An object of class “martTable”
Slot "id":
[1] "G1P2" "AGRN" "TNFRSF18" "TNFRSF4"

Slot "table":
$chromosome
[1] "1" "1" "1" "1"

$start
[1] 988946 995677 1178894 1186630

$end
[1] 989986 1031235 1182012 1189435


 > getFeature(chromosome=1, start=981787, end=1204439, 
type="entrezgene",mart=mart, species="hsapiens")
An object of class “martTable”
Slot "id":
[1] "9636" "375790" "54991" "254173" "8784" "7293"

Slot "table":
$chromosome
[1] "1" "1" "1" "1" "1" "1"

$start
[1] 988946 995677 1057128 1155000 1178894 1186630

$end
[1] 989986 1031235 1091398 1161164 1182012 1189435


You can query many types of idenifiers, refseq, ensembl ... for affy 
id's you have to do:

 > getFeature(chromosome=1, start=981787, end=1204439, 
array="hgu95av2",mart=mart)
An object of class “martTable”
Slot "id":
[1] "1107_s_at" "38432_at" "33454_at" "34916_s_at"

Slot "table":
$chromosome
[1] "1" "1" "1" "1"

$start
[1] 988946 988946 995677 1186630

$end
[1] 989986 989986 1031235 1189435

Cheers,
Steffen



Rifat Hamoudi wrote:

>Dear Steffen,
>			Please can you tell me if you if its possible to use biomaRt getGene()
>function to obtain all the gene IDs and names that are overlapped by a
>BAC/PAC. For example if I have a BAC say called "PAC14E10" would I be able
>to use getGene() to obtain all the genes within that BAC and if so can you
>give me example of the syntax of how I would do this.
>
>Many thanks in advance.
>
>Rifat
>
>
>  
>