Description: Fix spelling errors. hierachical -> hierarchical occurence -> occurrence acces -> access aaccession -> accession Author: Bas Couwenberg --- a/TFBS/PatternGen/YMF.pm +++ b/TFBS/PatternGen/YMF.pm @@ -177,7 +177,7 @@ sub _parse_stats_output{ my $motif =TFBS::PatternGen::YMF::Motif->new (-word=>$word, -tags => {z_score=>$z_score, - 'occurences'=>$occ, + 'occurrences'=>$occ, 'expectation value'=>$expect, 'variance'=>$var} ); @@ -190,4 +190,4 @@ sub _parse_stats_output{ } # -1; \ No newline at end of file +1; --- a/TFBS/MatrixSet.pm +++ b/TFBS/MatrixSet.pm @@ -763,7 +763,7 @@ sub _build_cluster { Title : cluster Usage : $matrixset->cluster(%args) Function: Clusters the matrices in the set - Returns : The root node of the hierachical clustering tree. + Returns : The root node of the hierarchical clustering tree. An integer specifying the optimal number of clusters. An array of TFBS::MatrixSets, one for each cluster. Args : Many: --- a/TFBS/Matrix/PFM.pm +++ b/TFBS/Matrix/PFM.pm @@ -366,7 +366,7 @@ sub to_ICM { # "pseudocounts" - standard pseudocount # correction, more suitable for # PFMs with large r column sums - # If the parameter is ommited, small + # If the parameter is omitted, small # sample correction is not applied -draw_error_bars # if true, adds error bars to each position --- a/TFBS/DB/JASPAR.pm +++ b/TFBS/DB/JASPAR.pm @@ -231,7 +231,7 @@ sub new { ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD, use the actual values. PASSWORD and USERNAME might be - optional, depending on the user's acces permissions for + optional, depending on the user's access permissions for the database server. =cut --- a/TFBS/DB/JASPAR2.pm +++ b/TFBS/DB/JASPAR2.pm @@ -237,7 +237,7 @@ sub new { ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD, use the actual values. PASSWORD and USERNAME might be - optional, depending on the user acces permissions for + optional, depending on the user access permissions for the database server. =cut @@ -263,7 +263,7 @@ sub connect { ("dbi:mysql:NEWDATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") In place of NEWDATABASENAME, HOSTNAME, USERNAME and PASSWORD use the actual values. PASSWORD and USERNAME - might be optional, depending on the users acces permissions + might be optional, depending on the users access permissions for the database server. =cut --- a/TFBS/DB/JASPAR4.pm +++ b/TFBS/DB/JASPAR4.pm @@ -188,7 +188,7 @@ sub new { ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD, use the actual values. PASSWORD and USERNAME might be - optional, depending on the user's acces permissions for + optional, depending on the user's access permissions for the database server. =cut --- a/TFBS/DB/JASPAR5.pm +++ b/TFBS/DB/JASPAR5.pm @@ -177,7 +177,7 @@ sub new { ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD, use the actual values. PASSWORD and USERNAME might be - optional, depending on the user's acces permissions for + optional, depending on the user's access permissions for the database server. =cut --- a/TFBS/DB/JASPAR6.pm +++ b/TFBS/DB/JASPAR6.pm @@ -178,7 +178,7 @@ sub new { ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD, use the actual values. PASSWORD and USERNAME might be - optional, depending on the user's acces permissions for + optional, depending on the user's access permissions for the database server. =cut --- a/TFBS/DB/JASPAR7.pm +++ b/TFBS/DB/JASPAR7.pm @@ -231,7 +231,7 @@ sub new { ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD, use the actual values. PASSWORD and USERNAME might be - optional, depending on the user's acces permissions for + optional, depending on the user's access permissions for the database server. =cut --- a/blib/lib/TFBS/DB/JASPAR2.pm +++ b/blib/lib/TFBS/DB/JASPAR2.pm @@ -237,7 +237,7 @@ sub new { ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD, use the actual values. PASSWORD and USERNAME might be - optional, depending on the user acces permissions for + optional, depending on the user access permissions for the database server. =cut @@ -263,7 +263,7 @@ sub connect { ("dbi:mysql:NEWDATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") In place of NEWDATABASENAME, HOSTNAME, USERNAME and PASSWORD use the actual values. PASSWORD and USERNAME - might be optional, depending on the users acces permissions + might be optional, depending on the users access permissions for the database server. =cut --- a/blib/lib/TFBS/DB/JASPAR4.pm +++ b/blib/lib/TFBS/DB/JASPAR4.pm @@ -188,7 +188,7 @@ sub new { ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD, use the actual values. PASSWORD and USERNAME might be - optional, depending on the user's acces permissions for + optional, depending on the user's access permissions for the database server. =cut --- a/blib/man3/TFBS::DB::JASPAR2.3pm +++ b/blib/man3/TFBS::DB::JASPAR2.3pm @@ -314,7 +314,7 @@ methods. Internal methods are preceded w \& ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") \& In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD, \& use the actual values. PASSWORD and USERNAME might be -\& optional, depending on the user acces permissions for +\& optional, depending on the user access permissions for \& the database server. .Ve .SS "create" @@ -332,7 +332,7 @@ methods. Internal methods are preceded w \& ("dbi:mysql:NEWDATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") \& In place of NEWDATABASENAME, HOSTNAME, USERNAME and \& PASSWORD use the actual values. PASSWORD and USERNAME -\& might be optional, depending on the users acces permissions +\& might be optional, depending on the users access permissions \& for the database server. .Ve .SS "dbh" --- a/TFBS/DB/LocalTRANSFAC.pm +++ b/TFBS/DB/LocalTRANSFAC.pm @@ -105,7 +105,7 @@ ENDNOTICE Title : get_Matrix_by_acc Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM'); - Function: fetches matrix data under the given TRANSFAC aaccession number + Function: fetches matrix data under the given TRANSFAC accession number from database and returns a TFBS::Matrix::* object Returns : a TFBS::Matrix::* object; the exact type of the object depending on the second argument (allowed --- a/TFBS/DB/TRANSFAC.pm +++ b/TFBS/DB/TRANSFAC.pm @@ -151,7 +151,7 @@ sub get_Matrix_by_ID { Title : get_Matrix_by_acc Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM'); - Function: fetches matrix data under the given TRANSFAC aaccession number + Function: fetches matrix data under the given TRANSFAC accession number from database and returns a TFBS::Matrix::* object Returns : a TFBS::Matrix::* object; the exact type of the object depending on the second argument (allowed --- a/blib/lib/TFBS/DB/LocalTRANSFAC.pm +++ b/blib/lib/TFBS/DB/LocalTRANSFAC.pm @@ -105,7 +105,7 @@ ENDNOTICE Title : get_Matrix_by_acc Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM'); - Function: fetches matrix data under the given TRANSFAC aaccession number + Function: fetches matrix data under the given TRANSFAC accession number from database and returns a TFBS::Matrix::* object Returns : a TFBS::Matrix::* object; the exact type of the object depending on the second argument (allowed --- a/blib/lib/TFBS/DB/TRANSFAC.pm +++ b/blib/lib/TFBS/DB/TRANSFAC.pm @@ -151,7 +151,7 @@ sub get_Matrix_by_ID { Title : get_Matrix_by_acc Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM'); - Function: fetches matrix data under the given TRANSFAC aaccession number + Function: fetches matrix data under the given TRANSFAC accession number from database and returns a TFBS::Matrix::* object Returns : a TFBS::Matrix::* object; the exact type of the object depending on the second argument (allowed --- a/blib/man3/TFBS::DB::LocalTRANSFAC.3pm +++ b/blib/man3/TFBS::DB::LocalTRANSFAC.3pm @@ -188,7 +188,7 @@ TFBS::DB::LocalTRANSFAC is a read only d .Vb 10 \& Title : get_Matrix_by_acc \& Usage : my $pfm = $db\->get_Matrix_by_acc(\*(AqV$CREB_01\*(Aq, \*(AqPFM\*(Aq); -\& Function: fetches matrix data under the given TRANSFAC aaccession number +\& Function: fetches matrix data under the given TRANSFAC accession number \& from database and returns a TFBS::Matrix::* object \& Returns : a TFBS::Matrix::* object; the exact type of the \& object depending on the second argument (allowed --- a/blib/man3/TFBS::DB::TRANSFAC.3pm +++ b/blib/man3/TFBS::DB::TRANSFAC.3pm @@ -217,7 +217,7 @@ retrieving a TFBS::Matrix::* object from .Vb 10 \& Title : get_Matrix_by_acc \& Usage : my $pfm = $db\->get_Matrix_by_acc(\*(AqV$CREB_01\*(Aq, \*(AqPFM\*(Aq); -\& Function: fetches matrix data under the given TRANSFAC aaccession number +\& Function: fetches matrix data under the given TRANSFAC accession number \& from database and returns a TFBS::Matrix::* object \& Returns : a TFBS::Matrix::* object; the exact type of the \& object depending on the second argument (allowed --- a/blib/man3/TFBS::DB::JASPAR4.3pm +++ b/blib/man3/TFBS::DB::JASPAR4.3pm @@ -256,7 +256,7 @@ methods. Internal methods are preceded w \& ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") \& In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD, \& use the actual values. PASSWORD and USERNAME might be -\& optional, depending on the user\*(Aqs acces permissions for +\& optional, depending on the user\*(Aqs access permissions for \& the database server. .Ve .SS "dbh" --- a/TFBS/Site.pm +++ b/TFBS/Site.pm @@ -54,7 +54,7 @@ TFBS::Site - a nucleotide sequence featu =head1 DESCRIPTION -TFBS::Site object holds data for a (possibly predicted) transcription factor binding site on a nucleotide sequence (start, end, strand, score, tags, as well as references to the corresponding sequence and pattern objects). TFBS::Site is a subclass of Bio::SeqFeature::Generic and has acces to all of its method. Additionally, it contains the pattern() method, an accessor for pattern object associated with the site object. +TFBS::Site object holds data for a (possibly predicted) transcription factor binding site on a nucleotide sequence (start, end, strand, score, tags, as well as references to the corresponding sequence and pattern objects). TFBS::Site is a subclass of Bio::SeqFeature::Generic and has access to all of its method. Additionally, it contains the pattern() method, an accessor for pattern object associated with the site object. =head1 FEEDBACK --- a/blib/lib/TFBS/Site.pm +++ b/blib/lib/TFBS/Site.pm @@ -54,7 +54,7 @@ TFBS::Site - a nucleotide sequence featu =head1 DESCRIPTION -TFBS::Site object holds data for a (possibly predicted) transcription factor binding site on a nucleotide sequence (start, end, strand, score, tags, as well as references to the corresponding sequence and pattern objects). TFBS::Site is a subclass of Bio::SeqFeature::Generic and has acces to all of its method. Additionally, it contains the pattern() method, an accessor for pattern object associated with the site object. +TFBS::Site object holds data for a (possibly predicted) transcription factor binding site on a nucleotide sequence (start, end, strand, score, tags, as well as references to the corresponding sequence and pattern objects). TFBS::Site is a subclass of Bio::SeqFeature::Generic and has access to all of its method. Additionally, it contains the pattern() method, an accessor for pattern object associated with the site object. =head1 FEEDBACK --- a/blib/man3/TFBS::Site.3pm +++ b/blib/man3/TFBS::Site.3pm @@ -173,7 +173,7 @@ TFBS::Site \- a nucleotide sequence feat .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" -TFBS::Site object holds data for a (possibly predicted) transcription factor binding site on a nucleotide sequence (start, end, strand, score, tags, as well as references to the corresponding sequence and pattern objects). TFBS::Site is a subclass of Bio::SeqFeature::Generic and has acces to all of its method. Additionally, it contains the \fIpattern()\fR method, an accessor for pattern object associated with the site object. +TFBS::Site object holds data for a (possibly predicted) transcription factor binding site on a nucleotide sequence (start, end, strand, score, tags, as well as references to the corresponding sequence and pattern objects). TFBS::Site is a subclass of Bio::SeqFeature::Generic and has access to all of its method. Additionally, it contains the \fIpattern()\fR method, an accessor for pattern object associated with the site object. .SH "FEEDBACK" .IX Header "FEEDBACK" Please send bug reports and other comments to the author.