Bio::Expression::FeatureGroup - a set of DNA/RNA features. ISA Bio::Expression::FeatureI
#
A set of DNA/RNA features.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
Allen Day <allenday@ucla.edu>
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : $featuregroup = Bio::Expression::FeatureGroup->new(%args); Function: create a new featuregroup object Returns : a Bio::Expression::FeatureGroup object Args : an optional hash of parameters to be used in initialization: -id -- the featuregroup ID -type -- the featuregroup type
Title : _initialize Usage : $featuregroup->_initialize(@args); Function: initialize the featuregroup object Returns : nothing Args : @args
Title : type Usage : $featuregroup->type($optional_arg); Function: get/set the type of the featuregroup Comments: this is probably going to be a string like "quality control", "mismatch blah blah", etc. Returns : the featuregroup type Args : a new value for the featuregroup type
Title : id Usage : $featuregroup->id($optional_arg); Function: get/set the id of the featuregroup Returns : the featuregroup id Args : a new value for the featuregroup id
Title : standard_deviation Usage : $featuregroup->standard_deviation($optional_arg); Function: get/set the standard deviation of the featuregroup value Returns : the featuregroup standard deviation Args : a new value for the featuregroup standard deviation Notes : this method does no calculation, it merely holds a value
Title : quantitation Usage : $featuregroup->quantitation($optional_arg); Function: get/set the quantitation of the featuregroup Returns : the featuregroup's quantitated value Args : a new value for the featuregroup's quantitated value Notes : this method does no calculation, it merely holds a value
Title : quantitation_units Usage : $featuregroup->quantitation_units($optional_arg); Function: get/set the quantitation units of the featuregroup Returns : the featuregroup's quantitated value units Args : a new value for the featuregroup's quantitated value units
Title : presence Usage : $featuregroup->presence($optional_arg); Function: get/set the presence call of the featuregroup Returns : the featuregroup's presence call Args : a new value for the featuregroup's presence call
Title : add_feature Usage : $feature_copy = $featuregroup->add_feature($feature); Function: add a feature to the featuregroup Returns : see this_feature() Args : a Bio::Expression::FeatureI compliant object
Title : this_feature Usage : $feature = $featuregroup->this_feature Function: access the last feature added to the featuregroup Returns : the last feature added to the featuregroup Args : none
Title : each_feature Usage : @features = $featuregroup->each_feature Function: returns a list of Bio::Expression::FeatureI compliant objects Returns : a list of objects Args : none
Title : each_feature_quantitation Usage : @featurequantitions = $featuregroup->each_feature_quantitation; Function: returns an list of quantitations of the features in the featuregroup Returns : a list of numeric values Args : none
Title : is_qc Usage : $is_quality_control = $featuregroup->is_qc Function: get/set whether or not the featuregroup is used for quality control purposes Returns : a boolean (equivalent) Args : a new value
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.