[Bioperl-l] Getting IC & Consensus with Bio::Matrix::PSM::SiteMatrix
ewijaya at singnet.com.sg
Sun Mar 13 22:04:40 EST 2005
Why my code below fails to return the IC values?
I thought the method is able to do that.
Is there anything I miss here?
My second question is about"consensus" method.
The consensus is generated by choosing the highest probability OR *N if
prob is too low*
1. How do you define when the probability is *too low*?
2. What is the reasoning behind this implementation?
e.g. Why my code below gives 'TANGTA' instead of "TATGTA"?
I find this particular module is very very useful.
I really wish I can make best use of it.
Thanks so much for your time.
Hope to hear from you again.
my @pA = (2,19,3,6,8,10);
my @pT = (7,3,6,2,20,5);
my @pC = (1,2,2,1,1,1);
my @pG = (3,1,1,9,8,7);
my %param =( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT);
my $site=new Bio::Matrix::PSM::SiteMatrix(%param);
my $consensus = $site->consensus;
my $ic = $site->IC; #Why it fails here?
print Dumper $ic;
print Dumper $consensus;
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