nuget
The PWM model
Probability
01 Syntax
SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Probability
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| E | 1 | 计算小样本校正项 e_n = 1 / (2 * ln(2) * n)，这个公式是用于对 Shannon 熵 进行小样本校正（small-sample correction）的经典项，常用于 motif 分析中 计算信息含量（Information Content）时，以减少因有限序列数量带来的偏差。 |
| CalculatesBits | 1 | The information content (y-axis) of position i is given by: Ri = log2(4) - (Hi + en) //nt Ri = log2(20) - (Hi + en) //prot 4 for DNA/RNA or 20 for protein. |
| HI | 1 |
03 Properties
04 Members
E(
Int32)计算小样本校正项 e_n = 1 / (2 ln(2) n)，这个公式是用于对 Shannon 熵 进行小样本校正（small-sample correction）的经典项，常用于 motif 分析中 计算信息含量（Information Content）时，以减少因有限序列数量带来的偏差。
Parameters
| Name | Type | Description |
|---|---|---|
nsize | Int32 | the count of the input fasta sequence. |
CalculatesBits(
Double, Double, Boolean)The information content (y-axis) of position i is given by:
Ri = log2(4) - (Hi + en) //nt
Ri = log2(20) - (Hi + en) //prot 4 for DNA/RNA or 20 for protein. Consequently, the maximum sequence conservation per site Is log2 4 = 2 bits for DNA/RNA And log2 20 ≈ 4.32 bits for proteins.
Parameters
| Name | Type | Description |
|---|---|---|
En | Double | e_n = \frac{1}{2 \ln(2) \cdot n} |
NtMol | Double | calculate for the nucleotide sequence model? |
HI(
Dictionary(Of Char, Double))Remarks
If n equals ZERO, then log2(0) is NaN, n Math.Log(n, 2) could not be measure, due to the reason of ZERO multiple any number is ZERO, so that if n is ZERO, then set n Math.Log(n, 2) its value to Zero directly.
Parameters
| Name | Type | Description |
|---|---|---|
f | Dictionary(Of Char, Double) | - |
region
the PWM matrix data
name
the unique id/name reference of the motif PWM model
width
motif residue number