File: TFBS%3A%3AMatrix%3A%3APFM.3pm

package info (click to toggle)
libtfbs-perl 0.7.1%2Bds-2
  • links: PTS, VCS
  • area: main
  • in suites: bookworm
  • size: 2,884 kB
  • sloc: perl: 10,728; ansic: 1,228; makefile: 563; sh: 9
file content (413 lines) | stat: -rw-r--r-- 13,760 bytes parent folder | download | duplicates (4)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
.\" Automatically generated by Pod::Man 2.23 (Pod::Simple 3.14)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is turned on, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.ie \nF \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    nr % 0
.    rr F
.\}
.el \{\
.    de IX
..
.\}
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
.IX Title "TFBS::Matrix::PFM 3"
.TH TFBS::Matrix::PFM 3 "2005-01-04" "perl v5.12.4" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
TFBS::Matrix::PFM \- class for raw position frequency matrix patterns
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.IP "\(bu" 4
creating a TFBS::Matrix::PFM object manually:
.Sp
.Vb 10
\&    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\en0 0 0 11 7 0\en0 9 12 0 0 0\en0 0 0 1 1 12";
\& 
\&    my $pfm = TFBS::Matrix::PFM\->new(\-matrixstring => $matrixstring,
\&                                     \-name         => "MyProfile",
\&                                     \-ID           => "M0001"
\&                                    );
.Ve
.IP "\(bu" 4
retrieving a TFBS::Matix::PFM object from a database:
.Sp
(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.)
.Sp
.Vb 6
\&    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");
.Ve
.IP "\(bu" 4
retrieving list of individual TFBS::Matrix::PFM objects
from a TFBS::MatrixSet object
.Sp
(See the TFBS::MatrixSet to learn how to create 
objects for storage and manipulation of multiple matrices.)
.Sp
.Vb 1
\&    my @pfm_list = $matrixset\->all_patterns(\-sort_by=>"name");
.Ve
.IP "\(bu" 4
convert a raw frequency matrix to other matrix types:
.Sp
.Vb 2
\&    my $pwm = $pfm\->to_PWM(); # convert to position weight matrix
\&    my $icm = $icm\->to_ICM(); # convert to information con
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
TFBS::Matrix::PFM is a class whose instances are objects representing
raw position frequency matrices (PFMs). A \s-1PFM\s0 is derived from N
nucleotide patterns of fixed size, e.g. the set of sequences
.PP
.Vb 12
\&    AGGCCT
\&    AAGCCT
\&    AGGCAT
\&    AAGCCT
\&    AAGCCT
\&    AGGCAT
\&    AGGCCT
\&    AGGCAT
\&    AGGTTT
\&    AGGCAT
\&    AGGCCT
\&    AGGCCT
.Ve
.PP
will give the matrix:
.PP
.Vb 4
\&    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 ]
.Ve
.PP
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.)
.PP
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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
Please send bug reports and other comments to the author.
.SH "AUTHOR \- Boris Lenhard"
.IX Header "AUTHOR - Boris Lenhard"
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
.SS "new"
.IX Subsection "new"
.Vb 5
\& 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 space\-delimited integers
\&              #or
\&           \-matrixfile,  # the name of a file containing four lines
\&                         # of tab\- or space\-delimited 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.
.Ve
.SS "column_sum"
.IX Subsection "column_sum"
.Vb 8
\& 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
.Ve
.SS "to_PWM"
.IX Subsection "to_PWM"
.Vb 9
\& 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
.Ve
.SS "to_ICM"
.IX Subsection "to_ICM"
.Vb 7
\& 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), \*(Aqschneider\*(Aq or \*(Aqpseudocounts\*(Aq
.Ve
.PP
How a \s-1PFM\s0 is converted to \s-1ICM:\s0
.PP
For a \s-1PFM\s0 element PFM[i,k], the probability without
pseudocounts is estimated to be simply
.PP
.Vb 1
\&  p[i,k] = PFM[i,k] / Z
.Ve
.PP
where 
\&\- Z equals the column sum of the matrix i.e. the number of motifs used
to construct the \s-1PFM\s0. 
\&\- 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)
.PP
Here is how one normally calculates the pseudocount-corrected positional
probability p'[i,j]:
.PP
.Vb 1
\&  p\*(Aq[i,k] = (PFM[i,k] + 0.25*sqrt(Z)) / (Z + sqrt(Z))
.Ve
.PP
0.25 is for the flat distribution of nucleotides, and sqrt(Z) is the
recommended pseudocount weight. In the general case,
.PP
.Vb 1
\&  p\*(Aq[i,k] = (PFM[i,k] + q[k]*B) / (Z + B)
.Ve
.PP
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).
.PP
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)):
.PP
\&\- for an arbitrary alphabet of A letters:
.PP
.Vb 1
\&  D[i] = log2(A) + sum_for_all_k(p[i,k]*log2(p[i,k]))
.Ve
.PP
\&\- special case for nucleotides (A=4)
.PP
.Vb 1
\&  D[i] = 2 + sum_for_all_k(p[i,k]*log2(p[i,k]))
.Ve
.PP
D[i] equals the information content of the position i in the motif. To
calculate the entire \s-1ICM\s0, you have to calculate the contrubution of each
nucleotide at a position i to D[i], i.e.
.PP
ICM[i,k] = p'[i,k] * D[i]
.SS "draw_logo"
.IX Subsection "draw_logo"
.Vb 10
\& 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; PFM\-specific 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
.Ve
.SS "add_PFM"
.IX Subsection "add_PFM"
.Vb 5
\& 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
.Ve
.SS "name"
.IX Subsection "name"
.SS "\s-1ID\s0"
.IX Subsection "ID"
.SS "class"
.IX Subsection "class"
.SS "matrix"
.IX Subsection "matrix"
.SS "length"
.IX Subsection "length"
.SS "revcom"
.IX Subsection "revcom"
.SS "rawprint"
.IX Subsection "rawprint"
.SS "prettyprint"
.IX Subsection "prettyprint"
The above methods are common to all matrix objects. Please consult
TFBS::Matrix to find out how to use them.