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.
|