[BioC] R: Script for filtering

Alberto Goldoni alberto.goldoni at segesta.pro
Thu Apr 23 16:10:39 CEST 2009

Sorry i'll be more detailed.

in R i'd need to load the file GenomeWideSNP_6.0 containing all the SNPs and in the second time i compare this list with a second list containing SNPs of 500 genes.

I would like to know how many genes (of the second list: 500) are included in the first list (GenomeWideSNP_6.0 database) and 
which SNPs are the same between the two lists.

best regards.

Da: James W. MacDonald [jmacdon at med.umich.edu]
Inviato: giovedì 23 aprile 2009 15.35
A: Alberto Goldoni
Cc: bioconductor at stat.math.ethz.ch
Oggetto: Re: [BioC] Script for filtering

Hi Alberto,

Alberto Goldoni wrote:
> Hi to everybody,
> i have to extract 500 genes from all the genes present on the GenomeWideSNP_6.0 database.

I'm not familiar with this database. Could you please give more
information? Also, there are no genes measured on the GenomeWideSNP_6.0
chip. This chip measures SNPs, which may or may not be in or near genes.

> If i have the list of these 500 genes, are there a script in order to extract only these genes from the complete list?

This question is too vague to be answered. What is the 'complete list'?

Maybe you are trying to subset a list or data.frame, in which case you
should look at

or perhaps



> Thanks a lot.
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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