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StatsHelpers.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Witold Wolski $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
38 #include <algorithm>
39 #include <cmath>
40 #include <complex>
41 #include <numeric>
42 #include <vector>
43 #include <cstddef>
44
45 namespace OpenSwath
46 {
47
51 OPENSWATHALGO_DLLAPI void normalize(const std::vector<double>& intensities, double normalization_factor, std::vector<double>& normalized_intensities);
52
56 template <typename T>
57 double norm(T beg, T end)
58 {
59 double res = 0.0;
60 for (; beg != end; ++beg)
61 {
62 double tmp = *beg;
63 res += tmp * tmp;
64 }
65 return sqrt(res);
66 }
67
68 struct mySqrt :
69 std::unary_function<double, double>
70 {
71 double operator()(double x)
72 {
73 return sqrt(x);
74 }
75
76 };
77
81 template <typename Texp, typename Ttheo>
82 double dotProd(Texp intExpBeg, Texp intExpEnd, Ttheo intTheo)
83 {
84 std::vector<double> res(std::distance(intExpBeg, intExpEnd));
85 std::transform(intExpBeg, intExpEnd, intTheo, res.begin(), std::multiplies<double>());
86 double sum = std::accumulate(res.begin(), res.end(), 0.);
87 return sum;
88 }
89
97 OPENSWATHALGO_DLLAPI double dotprodScoring(std::vector<double> intExp, std::vector<double> theorint);
98
102 template <typename Texp, typename Ttheo>
103 double manhattanDist(Texp itExpBeg, Texp itExpEnd, Ttheo itTheo)
104 {
105 double sum = 0.0;
106 for (std::size_t i = 0; itExpBeg < itExpEnd; ++itExpBeg, ++itTheo, ++i)
107 {
108 double x = *itExpBeg - *itTheo;
109 x = fabs(x);
110 sum += x;
111 }
112 return sum;
113 }
114
122 OPENSWATHALGO_DLLAPI double manhattanScoring(std::vector<double> intExp, std::vector<double> theorint);
123
124
128 template <typename TInputIterator, typename TInputIteratorY>
129 typename std::iterator_traits<TInputIterator>::value_type cor_pearson(
130 TInputIterator xBeg,
131 TInputIterator xEnd,
132 TInputIteratorY yBeg
133 )
134 {
135 typedef typename std::iterator_traits<TInputIterator>::value_type value_type;
136 value_type m1, m2;
137 value_type s1, s2;
138 value_type corr;
139 m1 = m2 = s1 = s2 = 0.0;
140 corr = 0.0;
141 ptrdiff_t n = std::distance(xBeg, xEnd);
142 value_type nd = static_cast<value_type>(n);
143 for (; xBeg != xEnd; ++xBeg, ++yBeg)
144 {
145 corr += *xBeg * *yBeg;
146 m1 += *xBeg;
147 m2 += *yBeg;
148 s1 += *xBeg * *xBeg;
149 s2 += *yBeg * *yBeg;
150 }
151 m1 /= nd;
152 m2 /= nd;
153 s1 -= m1 * m1 * nd;
154 s2 -= m2 * m2 * nd;
155
156 if (s1 < 1.0e-12 || s2 < 1.0e-12)
157 return 0.0;
158 else
159 {
160 corr -= m1 * m2 * (double)n;
161 corr /= sqrt(s1 * s2);
162 return corr;
163 }
164 }
165
169 class OPENSWATHALGO_DLLAPI mean_and_stddev
170 {
171 double m_, q_;
172 unsigned long c_;
173 public:
174 typedef double argument_type, result_type;
175 mean_and_stddev() :
176 m_(0.0), q_(0.0), c_(0u)
177 {
178 }
179
180 void operator()(double sample)
181 {
182 double const delta = sample - m_;
183 m_ += delta / ++c_;
184 q_ += delta * (sample - m_);
185 }
186
187 double sample_variance() const
188 {
189 return (c_ > 1u) ? (q_ / (c_ - 1)) : 0;
190 }
191
192 double standard_variance() const
193 {
194 return (c_ > 1u) ? (q_ / c_) : 0;
195 }
196
197 double sample_stddev() const
198 {
199 return std::sqrt(sample_variance());
200 }
201
202 double standard_stddev() const
203 {
204 return std::sqrt(standard_variance());
205 }
206
207 double mean() const
208 {
209 return m_;
210 }
211
212 unsigned long count() const
213 {
214 return c_;
215 }
216
217 double variance() const
218 {
219 return sample_variance();
220 }
221
222 double stddev() const
223 {
224 return sample_stddev();
225 }
226
227 double operator()() const
228 {
229 return stddev();
230 }
231
232 };
233
234 } //end namespace OpenSwath
235
OpenSwath::norm
double norm(T beg, T end)
compute the norm of the vector
Definition: StatsHelpers.h:57
OpenSwath::mean_and_stddev::standard_variance
double standard_variance() const
Definition: StatsHelpers.h:192
OpenSwath::mean_and_stddev::q_
double q_
Definition: StatsHelpers.h:171
OpenSwath
Definition: MRMScoring.h:49
OpenSwath::manhattanScoring
OPENSWATHALGO_DLLAPI double manhattanScoring(std::vector< double > intExp, std::vector< double > theorint)
manhattan scoring
OpenSwath::mySqrt::operator()
double operator()(double x)
Definition: StatsHelpers.h:71
OpenSwath::mean_and_stddev::operator()
void operator()(double sample)
Definition: StatsHelpers.h:180
OpenSwath::dotprodScoring
OPENSWATHALGO_DLLAPI double dotprodScoring(std::vector< double > intExp, std::vector< double > theorint)
the dot product scoring
OpenSwath::mean_and_stddev::result_type
double result_type
Definition: StatsHelpers.h:174
OpenSwath::mean_and_stddev::c_
unsigned long c_
Definition: StatsHelpers.h:172
OpenSwath::dotProd
double dotProd(Texp intExpBeg, Texp intExpEnd, Ttheo intTheo)
compute dotprod of vectors
Definition: StatsHelpers.h:82
OpenSwath::cor_pearson
std::iterator_traits< TInputIterator >::value_type cor_pearson(TInputIterator xBeg, TInputIterator xEnd, TInputIteratorY yBeg)
compute pearson correlation of vector x and y
Definition: StatsHelpers.h:129
OpenSwath::normalize
OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)
Normalize intensities in vector by normalization_factor.
OpenSwath::mean_and_stddev::mean
double mean() const
Definition: StatsHelpers.h:207
OpenSwath::mySqrt
Definition: StatsHelpers.h:68
OpenSwath::mean_and_stddev::variance
double variance() const
Definition: StatsHelpers.h:217
double
OpenSwath::mean_and_stddev::mean_and_stddev
mean_and_stddev()
Definition: StatsHelpers.h:175
OpenSwath::mean_and_stddev::stddev
double stddev() const
Definition: StatsHelpers.h:222
OpenSwath::mean_and_stddev::sample_variance
double sample_variance() const
Definition: StatsHelpers.h:187
OpenSwath::mean_and_stddev::count
unsigned long count() const
Definition: StatsHelpers.h:212
OpenSwath::mean_and_stddev::operator()
double operator()() const
Definition: StatsHelpers.h:227
OpenMS::Math::sum
static double sum(IteratorType begin, IteratorType end)
Calculates the sum of a range of values.
Definition: StatisticFunctions.h:120
OpenSwath::mean_and_stddev
functor to compute the mean and stddev of sequence using the std::foreach algorithm ...
Definition: StatsHelpers.h:169
OpenSwath::mean_and_stddev::sample_stddev
double sample_stddev() const
Definition: StatsHelpers.h:197
OpenSwath::mean_and_stddev::standard_stddev
double standard_stddev() const
Definition: StatsHelpers.h:202
OpenSwath::manhattanDist
double manhattanDist(Texp itExpBeg, Texp itExpEnd, Ttheo itTheo)
compute manhattan distance between Exp and Theo
Definition: StatsHelpers.h:103