|
|
Transfer Learning From Multiple Source Domains via Consensus Regularization
|
|
TFBS::Word::Consensus(3pm) User Contributed Perl Documentation TFBS::Word::Consensus(3pm) NAME
TFBS::Word - IUPAC DNA consensus word-based pattern class =head1 DESCRIPTION TFBS::Word is a base class consisting of universal constructor called by its subclasses (TFBS::Matrix::*), and word pattern manipulation methods that are independent of the word type. It is not meant to be instantiated itself. FEEDBACK
Please send bug reports and other comments to the author. AUTHOR - Boris Lenhard Boris Lenhard <Boris.Lenhard@cgb.ki.se> APPENDIX
The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore. new Title : new Usage : my $pwm = TFBS::Matrix::PWM->new(%args) Function: constructor for the TFBS::Matrix::PWM object Returns : a new TFBS::Matrix::PWM object Args : # you must specify the -word argument: -word, # a strig consisting of letters in # IUPAC degenerate DNA alphabet # (any of ACGTSWKMPYBDHVN) ####### -name, # string, OPTIONAL -ID, # string, OPTIONAL -class, # string, OPTIONAL -tags # a hash reference reference, OPTIONAL search_seq Title : search_seq Usage : my $siteset = $pwm->search_seq(%args) Function: scans a nucleotide sequence with the pattern represented by the PWM Returns : a TFBS::SiteSet object Args : # you must specify either one of the following three: -file, # the name od a fasta file (single sequence) #or -seqobj # a Bio::Seq object # (more accurately, a Bio::PrimarySeqobject or a # subclass thereof) #or -seqstring # a string containing the sequence -max_mismatches, # number of allowed positions in the site that do # not match the consensus # OPTIONAL: default 0 search_aln Title : search_aln Usage : my $site_pair_set = $pwm->search_aln(%args) Function: Scans a pairwise alignment of nucleotide sequences with the pattern represented by the word: it reports only those hits that are present in equivalent positions of both sequences and exceed a specified threshold score in both, AND are found in regions of the alignment above the specified conservation cutoff value. Returns : a TFBS::SitePairSet object Args : # you must specify either one of the following three: -file, # the name of the alignment file in Clustal format #or -alignobj # a Bio::SimpleAlign object # (more accurately, a Bio::PrimarySeqobject or a # subclass thereof) #or -alignstring # a multi-line string containing the alignment # in clustal format ############# -max_mismatches, # number of allowed positions in the site that do # not match the consensus # OPTIONAL: default 0 -window, # size of the sliding window (inn nucleotides) # for calculating local conservation in the # alignment # OPTIONAL: default 50 -cutoff # conservation cutoff (%) for including the # region in the results of the pattern search # OPTIONAL: default "70%" to_PWM validate_word length perl v5.14.2 2008-01-24 TFBS::Word::Consensus(3pm)
