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F102269005
ReferenceComputer.cpp
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Created
Tue, Feb 18, 23:01
Size
2 KB
Mime Type
text/x-c
Expires
Thu, Feb 20, 23:01 (2 d)
Engine
blob
Format
Raw Data
Handle
24320440
Attached To
R8820 scATAC-seq
ReferenceComputer.cpp
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#include <ReferenceComputer.hpp>
#include <Matrix2D.hpp>
#include <Matrix4D.hpp>
// some typdef
#include <typedef.hpp>
ReferenceComputer
::
ReferenceComputer
(
const
Matrix2D
<
int
>&
data
,
const
Matrix4D
<
double
>&
posterior_prob
,
size_t
n_threads
)
:
EMEngine
(
data
,
posterior_prob
.
get_dim
()[
1
],
1
,
posterior_prob
.
get_dim
()[
2
],
posterior_prob
.
get_dim
()[
3
]
==
2
,
EMEngine
::
seeding_codes
::
RANDOM
,
""
,
n_threads
)
{
// copy the data
this
->
data
=
matrix2d_i
(
this
->
n_row
,
v_i
(
this
->
n_col
))
;
for
(
size_t
i
=
0
;
i
<
this
->
n_row
;
i
++
)
{
for
(
size_t
j
=
0
;
j
<
this
->
n_col
;
j
++
)
{
this
->
data
[
i
][
j
]
=
data
(
i
,
j
)
;
}
}
// compute window means
this
->
window_mean
=
matrix2d_d
(
this
->
n_row
,
v_d
(
this
->
n_shift
,
0.
))
;
this
->
compute_window_means
()
;
// initialise, copy and compute probs
this
->
post_prob
=
matrix4d_d
(
this
->
n_row
,
matrix3d_d
(
this
->
n_class
,
matrix2d_d
(
this
->
n_shift
,
v_d
(
this
->
n_flip
,
0.
))))
;
this
->
class_prob
=
matrix3d_d
(
this
->
n_class
,
matrix2d_d
(
this
->
n_shift
,
v_d
(
this
->
n_flip
,
0.
)))
;
this
->
class_prob_tot
=
v_d
(
this
->
n_class
,
0.
)
;
this
->
post_prob_class
=
v_d
(
this
->
n_class
,
0.
)
;
for
(
size_t
i
=
0
;
i
<
this
->
n_row
;
i
++
)
{
for
(
size_t
j
=
0
;
j
<
this
->
n_class
;
j
++
)
{
for
(
size_t
s
=
0
;
s
<
this
->
n_shift
;
s
++
)
{
for
(
size_t
f
=
0
;
f
<
this
->
n_flip
;
f
++
)
{
double
p
=
posterior_prob
(
i
,
j
,
s
,
f
)
;
this
->
post_prob
[
i
][
j
][
s
][
f
]
=
p
;
this
->
post_prob_class
[
j
]
+=
p
;
this
->
post_prob_tot
+=
p
;
}
}
}
}
this
->
compute_class_prob
()
;
// compute the references
this
->
references
=
matrix2d_d
(
this
->
n_class
,
v_d
(
this
->
l_slice
,
0.
))
;
this
->
compute_references
()
;
}
ReferenceComputer
::~
ReferenceComputer
()
{
;
}
Matrix2D
<
double
>
ReferenceComputer
::
get_references
()
const
{
// add a 1st column with the class probabilities
Matrix2D
<
double
>
references
(
this
->
n_class
,
this
->
l_slice
+
1
,
0.
)
;
for
(
size_t
i
=
0
;
i
<
this
->
n_class
;
i
++
)
{
// class prob
references
(
i
,
0
)
=
this
->
class_prob_tot
[
i
]
;
// signal
for
(
size_t
j
=
0
;
j
<
this
->
l_slice
;
j
++
)
{
references
(
i
,
j
+
1
)
=
this
->
references
[
i
][
j
]
;
}
}
return
references
;
}
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