Summary Statistics
gentropy.dataset.summary_statistics.SummaryStatistics
dataclass
¶
Bases: Dataset
Summary Statistics dataset.
A summary statistics dataset contains all single point statistics resulting from a GWAS.
Source code in src/gentropy/dataset/summary_statistics.py
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|
exclude_region(region: str) -> SummaryStatistics
¶
Exclude a region from the summary stats dataset.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
region |
str
|
region given in "chr##:#####-####" format |
required |
Returns:
Name | Type | Description |
---|---|---|
SummaryStatistics |
SummaryStatistics
|
filtered summary statistics. |
Source code in src/gentropy/dataset/summary_statistics.py
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get_schema() -> StructType
classmethod
¶
Provides the schema for the SummaryStatistics dataset.
Returns:
Name | Type | Description |
---|---|---|
StructType |
StructType
|
Schema for the SummaryStatistics dataset |
Source code in src/gentropy/dataset/summary_statistics.py
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pvalue_filter(pvalue: float) -> SummaryStatistics
¶
Filter summary statistics based on the provided p-value threshold.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
pvalue |
float
|
upper limit of the p-value to be filtered upon. |
required |
Returns:
Name | Type | Description |
---|---|---|
SummaryStatistics |
SummaryStatistics
|
summary statistics object containing single point associations with p-values at least as significant as the provided threshold. |
Source code in src/gentropy/dataset/summary_statistics.py
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sanity_filter() -> SummaryStatistics
¶
The function filters the summary statistics by sanity filters.
The function filters the summary statistics by the following filters
- The p-value should not be eqaul 1.
- The beta and se should not be equal 0.
- The p-value, beta and se should not be NaN.
Returns:
Name | Type | Description |
---|---|---|
SummaryStatistics |
SummaryStatistics
|
The filtered summary statistics. |
Source code in src/gentropy/dataset/summary_statistics.py
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window_based_clumping(distance: int = 500000, gwas_significance: float = 5e-08) -> StudyLocus
¶
Generate study-locus from summary statistics using window-based clumping.
For more info, see WindowBasedClumping
Parameters:
Name | Type | Description | Default |
---|---|---|---|
distance |
int
|
Distance in base pairs to be used for clumping. Defaults to 500_000. |
500000
|
gwas_significance |
float
|
GWAS significance threshold. Defaults to 5e-8. |
5e-08
|
Returns:
Name | Type | Description |
---|---|---|
StudyLocus |
StudyLocus
|
Clumped study-locus optionally containing variants based on window. |
Source code in src/gentropy/dataset/summary_statistics.py
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Schema¶
root
|-- studyId: string (nullable = false)
|-- variantId: string (nullable = false)
|-- chromosome: string (nullable = false)
|-- position: integer (nullable = false)
|-- beta: double (nullable = false)
|-- sampleSize: integer (nullable = true)
|-- pValueMantissa: float (nullable = false)
|-- pValueExponent: integer (nullable = false)
|-- effectAlleleFrequencyFromSource: float (nullable = true)
|-- standardError: double (nullable = true)