How To Provide Background File In Go Term Finder

Question

[Fatcat]

I use GO::TermFinder and want to provide a list of genes for the background population instead of using the default one, does anybody known how to do that?

Answer 1

[User 59]

You can use this (information from http://search.cpan.org/~sherlock/GO-TermFinder-0.86/lib/GO/TermFinder.pm):

Usage (use a subset of genes as the background population):

my $termFinder = GO::TermFinder->new(annotationProvider=> $annotationProvider,
                                     ontologyProvider  => $ontologyProvider,
                                     population        => \@genes,
                                     aspect            => <P|C|F>);

What is important for you is the "population"

"This argument allows a client to indicate the population that should used to calculate a background distribution of GO terms. In the absence of population argument, then the background distribution will be drawn from all genes in the annotationProvider. This should be provided as an array reference, and no ambiguous names should be provided (see AnnotationProvider for details of name ambiguity). This option is particularly pertinent in a case where for example you assayed only 2000 genes in a two hybrid experiment, and found 20 interesting ones. To find significant terms, you need to do it in the context of the genes that you assayed, not in the context of all genes with annotation."

[Fatcat]

Thank you very much, and it really works well!

[Dejian]

Great! It is puzzling me now.