[BioMart Users] biomart and inverse selection

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[BioMart Users] biomart and inverse selection

andrea_bio
Hi

IS there a feature of biomart which enables you to retrieve everything
other than the objects that match your filters, a sort of inverse
selection feature. It probably doesn't come up that much but a common
example when investigating a disease might be get me all the SNPs in
this set of candidate genes that are NOT in dbSNP

thanks a lot
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Re: [BioMart Users] biomart and inverse selection

Joachim Baran-2
Hi!

On 11-03-28 7:08 PM, "Andrea Edwards" <[hidden email]> wrote:
>IS there a feature of biomart which enables you to retrieve everything
>other than the objects that match your filters, a sort of inverse
>selection feature. It probably doesn't come up that much but a common
>example when investigating a disease might be get me all the SNPs in
>this set of candidate genes that are NOT in dbSNP
  You are probably referring to the "Limit to genes..." type of filter as
it is present in the Ensembl marts (www.biomart.org, Ensembl Genes,
Filters -> GENE: -> "Limit to genes..." -> "Only" / "Excluded"). Such a
switch is not available in BioMart 0.8 anymore.

  In BioMart 0.8 you can set a multi-select filter instead. A multi-select
filter shows you a list of values that you can filter on and you are free
to pick an arbitrary number of them for filtering (in 0.7, you can see an
example on www.biomart.org, Ensembl Genes, Filters -> GENE: -> "Gene type"
-> "miRNA" / "miscRNA" / etc.). So, you could provide a list of the
possible datasources, where "dbSNP" is one of them, and the user would
then select every entry in that multi-select filter *except* "dbSNP" to
get the results for everything but not dbSNP entries.

  Here is how you configure it in MartConfigurator:
  1. Make a copy of the filter that applies to the column that contains
"dbSNP" among other values
  2. Set the filter's property "type" to "multiSelect"
  3. Right-click onto the filter in the tree-view and choose "Dropdown
list"
  4. In the "Filter DropDown Dialog" window that pops up, click on "Add"
  5. In the tiny unnamed window that pops up, copy & paste the values you
would like to filter on
    - each value you would like to filter on has to appear on a separate
row
    - do not worry if your text exceeds the visible text-area; it is still
saved
    - only have plain ASCII names as filter values, no punctuation; e.g.
"dbSNP" would be one of the values
    - you can obtain the list of possible filter-values for that column by
running "SELECT DISTINCT(your_columnname) FROM ..." on your database
  6. Click on "OK"
  7. You should now see a list of the values you set in "Filter DropDown
Dialog", with one value per line
  7. Click on "Save"
  8. Save your configuration
  9. Restart your deployed BioMart with: ./dist/scripts/biomart-server.sh
restart

Joachim

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