[BioC] biomaRt getFeature function

[steffen at stat.Berkeley.EDU]

Hi Paul,

getFeature has been removed a few versions ago as it contained a lot of
hard-coded code.  The main query function in biomaRt is getBM, this is a
very general function which allows you to do any possible query to BioMart
systems that are within one dataset.

For your problem I would retrieve all Ensembl gene locations and use that
output to iterate over to figure out which of your fragments are in genes
or which is the closest gene to your fragments.

So you need one biomaRt query which will retrieve all ensembl gene
coordinates:

library(biomaRt)
ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl")
geneLocs =
getBM(c("ensembl_gene_id","strand","chromosome_name","start_position","end_position"),
mart=ensembl)

Cheers,
Steffen







> Dear folks,
>
> I've installed the package biomaRt currently and I tried to use the
> function "getFeature". But I had to notice that this function does not
> exist. So since what time is that function removed from the package and
> is there now a comparable function?
>
> By the way I try to get out following. I have a lot of dna fragments. I
> know from every fragment the location on the genome (chromosom, start
> and end base position). Now I would like to know if a fragment is
> located directly in a gene (that would be easy with the getFeature
> function from biomaRt :) ). If a fragment is not located in a gene I
> would like to get out which and where the next gene is located upstream
> and downstream. Normally I would code a simple perl script which would
> compare the fragment positions with the annotated cDNA positions but I
> want to do it in R because all my other analysis I've done also in R.
> Maybe somebody knows a easy trick to solve my question...
>
> Thanks in advance,
> Paul
>
>  > sessionInfo()
> R version 2.8.0 (2008-10-20)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] brainwaver_1.4       waveslim_1.6.1       exonmap_2.0.0
>  [4] RMySQL_0.6-1         DBI_0.2-4            RColorBrewer_1.0-2
>  [7] genefilter_1.20.0    survival_2.34-1      biomaRt_1.16.0
> [10] affy_1.18.1          preprocessCore_1.2.1 affyio_1.8.0
> [13] HELP_1.0.0           Biobase_2.0.1
>
> loaded via a namespace (and not attached):
> [1] annotate_1.18.0     AnnotationDbi_1.2.1 RCurl_0.91-0
> [4] RSQLite_0.7-0       XML_1.98-1
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>