SYNOPSIS

creating a TFBS::Matrix::PFM object manually:
my $matrixref = [ [ 12, 3, 0, 0, 4, 0 ],
[ 0, 0, 0, 11, 7, 0 ],
[ 0, 9, 12, 0, 0, 0 ],
[ 0, 0, 0, 1, 1, 12 ]
];
my $pfm = TFBS::Matrix::PFM>new(matrix => $matrixref,
name => "MyProfile",
ID => "M0001"
);
# or
my $matrixstring =
"12 3 0 0 4 0\n0 0 0 11 7 0\n0 9 12 0 0 0\n0 0 0 1 1 12";
my $pfm = TFBS::Matrix::PFM>new(matrixstring => $matrixstring,
name => "MyProfile",
ID => "M0001"
); 
retrieving a TFBS::Matix::PFM object from a database:
(See documentation of individual TFBS::DB::* modules to learn how to connect to different types of pattern databases and retrieve TFBS::Matrix::* objects from them.)
my $db_obj = TFBS::DB::JASPAR2>new (connect => ["dbi:mysql:JASPAR2:myhost", "myusername", "mypassword"]); my $pfm = $db_obj>get_Matrix_by_ID("M0001", "PFM"); # or my $pfm = $db_obj>get_Matrix_by_name("MyProfile", "PFM");

retrieving list of individual TFBS::Matrix::PFM objects
from a TFBS::MatrixSet object
(See the TFBS::MatrixSet to learn how to create objects for storage and manipulation of multiple matrices.)
my @pfm_list = $matrixset>all_patterns(sort_by=>"name");

convert a raw frequency matrix to other matrix types:
my $pwm = $pfm>to_PWM(); # convert to position weight matrix my $icm = $icm>to_ICM(); # convert to information con
DESCRIPTION
TFBS::Matrix::PFM is a class whose instances are objects representing raw position frequency matrices (PFMs). A PFM is derived from N nucleotide patterns of fixed size, e.g. the set of sequences
AGGCCT AAGCCT AGGCAT AAGCCT AAGCCT AGGCAT AGGCCT AGGCAT AGGTTT AGGCAT AGGCCT AGGCCT
will give the matrix:
A:[ 12 3 0 0 4 0 ] C:[ 0 0 0 11 7 0 ] G:[ 0 9 12 0 0 0 ] T:[ 0 0 0 1 1 12 ]
which contains the count of each nucleotide at each position in the sequence. (If you have a set of sequences as above and want to create a TFBS::Matrix::PFM object out of them, have a look at TFBS::PatternGen::SimplePFM module.)
PFMs are easily converted to other types of matrices, namely information content matrices and position weight matrices. A TFBS::Matrix::PFM object has the methods to_ICM and to_PWM which do just that, returning a TFBS::Matrix::ICM and TFBS::Matrix::PWM objects, respectively.
FEEDBACK
Please send bug reports and other comments to the author.AUTHOR  Boris Lenhard
Boris Lenhard <[email protected]>APPENDIX
The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore.new
Title : new Usage : my $pfm = TFBS::Matrix::PFM>new(%args) Function: constructor for the TFBS::Matrix::PFM object Returns : a new TFBS::Matrix::PFM object Args : # you must specify either one of the following three: matrix, # reference to an array of arrays of integers #or matrixstring,# a string containing four lines # of tab or spacedelimited integers #or matrixfile, # the name of a file containing four lines # of tab or spacedelimited integers ####### name, # string, OPTIONAL ID, # string, OPTIONAL class, # string, OPTIONAL tags # an array reference, OPTIONAL Warnings : Warns if the matrix provided has columns with different sums. Columns with different sums contradict the usual origin of matrix data and, unless you are absolutely sure that column sums _should_ be different, it would be wise to check your matrices.
column_sum
Title : column_sum Usage : my $nr_sequences = $pfm>column_sum() Function: calculates the sum of elements of one column (the first one by default) which normally equals the number of sequences used to derive the PFM. Returns : the sum of elements of one column (an integer) Args : columnn number (starting from 1), OPTIONAL  you DO NOT need to specify it unless you are dealing with a matrix
to_PWM
Title : to_PWM Usage : my $pwm = $pfm>to_PWM() Function: converts a raw frequency matrix (a TFBS::Matrix::PFM object) to position weight matrix. At present it assumes uniform background distribution of nucleotide frequencies. Returns : a new TFBS::Matrix::PWM object Args : none; in the future releases, it should be able to accept a user defined background probability of the four nucleotides
to_ICM
Title : to_ICM Usage : my $icm = $pfm>to_ICM() Function: converts a raw frequency matrix (a TFBS::Matrix::PFM object) to information content matrix. At present it assumes uniform background distribution of nucleotide frequencies. Returns : a new TFBS::Matrix::ICM object Args : small_sample_correction # undef (default), 'schneider' or 'pseudocounts'
How a PFM is converted to ICM:
For a PFM element PFM[i,k], the probability without pseudocounts is estimated to be simply
p[i,k] = PFM[i,k] / Z
where  Z equals the column sum of the matrix i.e. the number of motifs used to construct the PFM.  i is the column index (position in the motif)  k is the row index (a letter in the alphacer, here k is one of (A,C,G,T)
Here is how one normally calculates the pseudocountcorrected positional probability p'[i,j]:
p'[i,k] = (PFM[i,k] + 0.25*sqrt(Z)) / (Z + sqrt(Z))
0.25 is for the flat distribution of nucleotides, and sqrt(Z) is the recommended pseudocount weight. In the general case,
p'[i,k] = (PFM[i,k] + q[k]*B) / (Z + B)
where q[k] is the background distribution of the letter (nucleotide) k, and B an arbitrary pseudocount value or expression (for no pseudocounts B=0).
For a given position i, the deviation from random distribution in bits is calculated as (Baldi and Brunak eq. 1.9 (2ed) or 1.8 (1ed)):
 for an arbitrary alphabet of A letters:
D[i] = log2(A) + sum_for_all_k(p[i,k]*log2(p[i,k]))
 special case for nucleotides (A=4)
D[i] = 2 + sum_for_all_k(p[i,k]*log2(p[i,k]))
D[i] equals the information content of the position i in the motif. To calculate the entire ICM, you have to calculate the contrubution of each nucleotide at a position i to D[i], i.e.
ICM[i,k] = p'[i,k] * D[i]
draw_logo
Title : draw_logo Usage : my $gd_image = $pfm>draw_logo() Function: draws a sequence logo; similar to the method in TFBS::Matrix::ICM, but can automatically calculate error bars for drawing Returns : a GD image object (see documentation of GD module) Args : many; PFMspecific options are: small_sample_correction # One of # "Schneider" (uses correction # described by Schneider et al. # (Schneider t et al. (1986) J.Biol.Chem. # "pseudocounts"  standard pseudocount # correction, more suitable for # PFMs with large r column sums # If the parameter is ommited, small # sample correction is not applied draw_error_bars # if true, adds error bars to each position # in the logo. To calculate the error bars, # it uses the small_sample_connection # argument if explicitly set, # or "Schneider" by default For other args, see draw_logo entry in TFBS::Matrix::ICM documentation
add_PFM
Title : add_PFM Usage : $pfm>add_PFM($another_pfm) Function: adds the values of $pnother_pfm matrix to $pfm Returns : reference to the updated $pfm object Args : a TFBS::Matrix::PFM object
name
ID
class
matrix
length
revcom
rawprint
prettyprint
The above methods are common to all matrix objects. Please consult TFBS::Matrix to find out how to use them.