scran_blocks
Blocking utilities for libscran
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Blocking utilities for libscran. More...
Classes | |
struct | VariableWeightParameters |
Parameters for compute_variable_weight() . More... | |
Enumerations | |
enum class | WeightPolicy : char { NONE , SIZE , VARIABLE , EQUAL } |
Functions | |
template<typename Stat_ , typename Output_ > | |
void | average_vectors (const std::size_t n, std::vector< Stat_ * > in, Output_ *const out, const bool skip_nan) |
template<typename Output_ = double, typename Stat_ > | |
std::vector< Output_ > | average_vectors (const std::size_t n, std::vector< Stat_ * > in, const bool skip_nan) |
template<typename Stat_ , typename Weight_ , typename Output_ > | |
void | average_vectors_weighted (const std::size_t n, std::vector< Stat_ * > in, const Weight_ *const w, Output_ *const out, const bool skip_nan) |
template<typename Output_ = double, typename Stat_ , typename Weight_ > | |
std::vector< Output_ > | average_vectors_weighted (const std::size_t n, std::vector< Stat_ * > in, const Weight_ *const w, const bool skip_nan) |
double | compute_variable_weight (const double s, const VariableWeightParameters ¶ms) |
template<typename Size_ , typename Weight_ > | |
void | compute_weights (const std::size_t num_blocks, const Size_ *const sizes, const WeightPolicy policy, const VariableWeightParameters &variable, Weight_ *const weights) |
template<typename Weight_ = double, typename Size_ > | |
std::vector< Weight_ > | compute_weights (const std::vector< Size_ > &sizes, const WeightPolicy policy, const VariableWeightParameters &variable) |
template<typename Input_ > | |
std::remove_cv_t< std::remove_reference_t< Input_ > > | I (Input_ x) |
Blocking utilities for libscran.
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strong |
Policy for weighting blocks based on their size, i.e., the number of cells in each block. This determines the nature of the weight calculations in compute_weights()
.
SIZE
: blocks are weighted in proportion to their size. Larger blocks will contribute more to the weighted average.EQUAL
: each non-empty block is assigned equal weight, regardless of its size. Equivalent to averaging across non-empty blocks without weights.VARIABLE
: each batch is weighted using the logic in compute_variable_weight()
. This penalizes small blocks with unreliable statistics while equally weighting all large blocks.NONE
: a deprecated alias for SIZE
. std::vector< Output_ > scran_blocks::average_vectors | ( | const std::size_t | n, |
std::vector< Stat_ * > | in, | ||
const bool | skip_nan ) |
Overload of compute()
that allocates an output vector of averaged values.
Output | Floating-point output type. |
Stat | Type of the input statistic, typically floating point. |
n | Length of each array. | |
[in] | in | Vector of pointers to input arrays of length n . |
skip_nan | Whether to check for NaNs. |
n
is returned, containing the average of all arrays in in
. Specifically, the i
-th entry is set to the average of the i
-th entry across all in
arrays. void scran_blocks::average_vectors | ( | const std::size_t | n, |
std::vector< Stat_ * > | in, | ||
Output_ *const | out, | ||
const bool | skip_nan ) |
Average parallel elements across multiple arrays. This is equivalent to calling average_weighted_vectors()
with equal weights for each array.
Stat_ | Type of the input statistic, typically floating point. |
Output_ | Floating-point output type. |
n | Length of each array. | |
[in] | in | Vector of pointers to input arrays of length n . |
[out] | out | Pointer to an output array of length n . On completion, out is filled with the average of all arrays in in . Specifically, the i -th entry of out is set to the average of the i -th entry across all in arrays. |
skip_nan | Whether to check for NaNs. If true , NaNs are ignored in the average calculations for each element, at the cost of some efficiency. |
std::vector< Output_ > scran_blocks::average_vectors_weighted | ( | const std::size_t | n, |
std::vector< Stat_ * > | in, | ||
const Weight_ *const | w, | ||
const bool | skip_nan ) |
Overload of average_vectors_weighted()
that allocates an output vector of averaged values.
Output_ | Floating-point output type. |
Weight_ | Type of the weight, typically floating point. |
Stat_ | Type of the input statistic, typically floating point. |
n | Length of each array. | |
[in] | in | Vector of pointers to input arrays of the same length. |
[in] | w | Pointer to an array of length equal to in.size() , containing the weight to use for each input array. Weights should be non-negative and finite. |
skip_nan | Whether to check for NaNs. |
in
. void scran_blocks::average_vectors_weighted | ( | const std::size_t | n, |
std::vector< Stat_ * > | in, | ||
const Weight_ *const | w, | ||
Output_ *const | out, | ||
const bool | skip_nan ) |
Compute a weighted average of parallel elements across multiple arrays. For example, we can average statistics across blocks using weights computed with compute_weights()
.
Stat_ | Type of the input statistic, typically floating point. |
Weight_ | Type of the weight, typically floating point. |
Output_ | Floating-point output type. |
n | Length of each array. | |
[in] | in | Vector of pointers to input arrays of length n . |
[in] | w | Pointer to an array of length equal to in.size() , containing the weight to use for each input array. Weights should be non-negative and finite. |
[out] | out | Pointer to an output array of length n . On output, out is filled with the weighted average of all arrays in in . Specifically, the i -th entry of out is set to the average of the i -th entry across all in arrays. |
skip_nan | Whether to check for NaNs. If true , NaNs are ignored in the average calculations for each element, at the cost of some efficiency. |
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inline |
Assign a variable weight to each block of cells, for use in computing a weighted average across blocks. The weight for each block is calculated from the size of that block.
VariableWeightParameters::lower_bound
, it has zero weight.VariableWeightParameters::upper_bound
, it has weight of 1.Blocks that are "large enough" (i.e., above the upper bound) are considered to be equally trustworthy and receive the same weight, ensuring that each block contributes equally to the weighted average. By comparison, very small blocks receive lower weight as their statistics are generally less stable.
s | Size of the block, in terms of the number of cells in that block. |
params | Parameters for the weight calculation, consisting of the lower and upper bounds. |
void scran_blocks::compute_weights | ( | const std::size_t | num_blocks, |
const Size_ *const | sizes, | ||
const WeightPolicy | policy, | ||
const VariableWeightParameters & | variable, | ||
Weight_ *const | weights ) |
Compute weights for multiple blocks based on their size and the weighting policy. For variable weights, this function will call compute_variable_weight()
for each block.
Weights should be interpreted as relative values within a single compute_weights()
call, i.e., weights from different calls may not be comparable. They are typically used in functions like average_weighted_vectors()
to compute a weighted average of statistics across blocks.
Size_ | Numeric type of the block size. |
Weight_ | Floating-point type of the output weights. |
num_blocks | Number of blocks. | |
[in] | sizes | Pointer to an array of length num_blocks , containing the size of each block. |
policy | Policy for weighting blocks of different sizes. | |
variable | Parameters for the variable block weights. | |
[out] | weights | Pointer to an array of length num_blocks . On output, this is filled with the weight of each block. |
std::vector< Weight_ > scran_blocks::compute_weights | ( | const std::vector< Size_ > & | sizes, |
const WeightPolicy | policy, | ||
const VariableWeightParameters & | variable ) |
A convenience overload for compute_weights()
that accepts and returns vectors.
Size_ | Numeric type of the block size. |
Weight_ | Floating-point type of the output weights. |
sizes | Vector containing the size of each block. |
policy | Policy for weighting blocks of different sizes. |
variable | Parameters for the variable block weights. |