Description: Fix spelling errors. classs -> class hierachical -> hierarchical infromation -> information occurence -> occurrence repective -> respective supresses -> suppresses taht -> that Author: Bas Couwenberg --- a/TFBS/DB/JASPAR2.pm +++ b/TFBS/DB/JASPAR2.pm @@ -458,7 +458,7 @@ gives a set of PWMs whose (structural cl OR 'Mus musculus'). The -min_ic filter is applied after the query in the sense that the -matrices profiles with total infromation content less than specified +matrices profiles with total information content less than specified are not included in the set. =cut --- a/TFBS/DB/JASPAR4.pm +++ b/TFBS/DB/JASPAR4.pm @@ -409,7 +409,7 @@ sub get_Matrix_by_name { database storage, any tag can be used for information retrieval. Additionally, arguments as 'name' and 'class' can be used (even though they are not tags. - As with get_Matrix methods, it is important to realize taht any matrix + As with get_Matrix methods, it is important to realize that any matrix format can be stored in the database: the TFBS::MatrixSet might therefore consist of PFMs, ICMs and PWMS, depending on how matrices are stored, @@ -445,7 +445,7 @@ gives a set of TFBS::Matrix::PFM objects from is 'Homo sapiens'OR 'Mus musculus'). The -min_ic filter is applied after the query in the sense that the -matrices profiles with total infromation content less than specified +matrices profiles with total information content less than specified are not included in the set. =cut --- a/TFBS/PatternGen.pm +++ b/TFBS/PatternGen.pm @@ -14,7 +14,7 @@ TFBS::PatternGen - a base class for patt =head1 DESCRIPTION -TFBS::PatternGen is a base classs providing methods common to all pattern generating +TFBS::PatternGen is a base class providing methods common to all pattern generating modules. It is meant to be inherited by a concrete pattern generator, which must have its own constructor. --- a/TFBS/Matrix/ICM.pm +++ b/TFBS/Matrix/ICM.pm @@ -98,7 +98,7 @@ following information content matrix: G:[0.00 0.89 2.00 0.00 0.00 0.00] T:[0.00 0.00 0.00 0.13 0.06 2.00] -which contains the "weights" associated with the occurence of each +which contains the "weights" associated with the occurrence of each nucleotide at the given position in a pattern. A TFBS::Matrix::PWM object is equipped with methods to search nucleotide --- a/TFBS/Matrix/PWM.pm +++ b/TFBS/Matrix/PWM.pm @@ -100,7 +100,7 @@ following position weight matrix: G:[-1.57 1.85 -2.57 -1.34 -1.57 1.14] T:[ 0.31 -3.16 -2.57 1.76 0.24 -0.83] -which contains the "weights" associated with the occurence of each +which contains the "weights" associated with the occurrence of each nucleotide at the given position in a pattern. A TFBS::Matrix::PWM object is equipped with methods to search nucleotide --- a/TFBS/PatternGen/Elph.pm +++ b/TFBS/PatternGen/Elph.pm @@ -66,7 +66,7 @@ use Bio::SeqIO; Other arguments are: -binary # a fully qualified path to Gibbs executable # OPTIONAL: default 'Gibbs' - -nr_hits # a presumed number of pattern occurences in the + -nr_hits # a presumed number of pattern occurrences in the # sequence set: it can be a single integer, e.g. # -nr_hits => 24 , or a reference to an array of # integers, e.g -nr_hits => [12, 24, 36] --- a/TFBS/PatternGen/Gibbs.pm +++ b/TFBS/PatternGen/Gibbs.pm @@ -67,7 +67,7 @@ use Bio::SeqIO; Other arguments are: -binary # a fully qualified path to Gibbs executable # OPTIONAL: default 'Gibbs' - -nr_hits # a presumed number of pattern occurences in the + -nr_hits # a presumed number of pattern occurrences in the # sequence set: it can be a single integer, e.g. # -nr_hits => 24 , or a reference to an array of # integers, e.g -nr_hits => [12, 24, 36] --- 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/Matrix/Alignment.pm +++ b/TFBS/Matrix/Alignment.pm @@ -239,7 +239,7 @@ sub new { Title : alignment Usage : my $alignment_string = $alignmentobject->alignment(); Function: access a string describing the alignment - Returns : an string, where each number refers to a position in repective PFM. + Returns : an string, where each number refers to a position in respective PFM. Position numbering is according to orientation: ie if the second profile is reversed, position 1 corresponds to the last position in the input profile. Gaps are denoted as - . --- a/TFBS/DB/LocalTRANSFAC.pm +++ b/TFBS/DB/LocalTRANSFAC.pm @@ -70,7 +70,7 @@ use TFBS::Matrix::PFM; # have read and accepted the terms # of use of TRANSFAC at # http://transfac.gbf.de/TRANSFAC/disclaimer.htm; - # this also supresses the annoying + # this also suppresses the annoying # message that is printed to STDERR # upon invoking the method --- a/TFBS/DB/TRANSFAC.pm +++ b/TFBS/DB/TRANSFAC.pm @@ -69,7 +69,7 @@ use LWP::Simple qw($ua get); # have read and accepted the terms # of use of TRANSFAC at # http://transfac.gbf.de/TRANSFAC/disclaimer.htm; - # this also supresses the annoying + # this also suppresses the annoying # message that is printed to STDERR # upon invoking the method --- 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: