Bio::Variation::SNP - submitted SNP $SNP = Bio::Variation::SNP->new (); Inherits from Bio::Variation::SeqDiff and Bio::Variation::Allele, with additional methods that are (db)SNP specific (ie, refSNP/subSNP IDs, batch IDs, validation methods).

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists

Reporting Bugs
report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Allen Day <allenday@ucla.edu> The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

get/set-able methods
Usage : $is = $snp->method() Function: for getting/setting attributes Returns : a value. probably a scalar. Args : if you're trying to set an attribute, pass in the new value. Methods: -------- id type observed seq_5 seq_3 ncbi_build ncbi_chr_hits ncbi_ctg_hits ncbi_seq_loc ucsc_build ucsc_chr_hits ucsc_ctg_hits heterozygous heterozygous_SE validated genotype handle batch_id method locus_id symbol mrna protein functional_class

is_subsnp
Title : is_subsnp Usage : $is = $snp->is_subsnp() Function: returns 1 if $snp is a subSNP Returns : 1 or undef Args : NONE

subsnp
Title : subsnp Usage : $subsnp = $snp->subsnp() Function: returns the currently active subSNP of $snp Returns : Bio::Variation::SNP Args : NONE

add_subsnp
Title : add_subsnp Usage : $subsnp = $snp->add_subsnp() Function: pushes the previous value returned by subsnp() onto a stack, accessible with each_subsnp(). Sets return value of subsnp() to a new Bio::Variation::SNP object, and returns that object. Returns : Bio::Varitiation::SNP Args : NONE

each_subsnp
Title : each_subsnp Usage : @subsnps = $snp->each_subsnp() Function: returns a list of the subSNPs of a refSNP Returns : list Args : NONE