Methods
add(other) → {*}
Combine this set of score statistics with another. See also https://genome.sph.umich.edu/wiki/RAREMETAL_METHOD#SINGLE_VARIANT_META_ANALYSIS for information on how statistics are combined.
Parameters:
| Name | Type | Description |
|---|---|---|
other |
ScoreStatTable | Another set of score statistics with which to combine this object for the purposes of meta-analysis. |
Returns:
No object is returned; this method runs in-place.
- Type
- *
appendScore(variant, position, u, v, altFreq, ea, eaFreq, pvalue)
Add a variant and relevant data on it into the table.
Parameters:
| Name | Type | Description |
|---|---|---|
variant |
string | Variant (chr:pos_ref/alt) |
position |
number | Integer position of variant |
u |
number | Score statistic |
v |
number | Variance of score statistic |
altFreq |
number | Alternate allele frequency |
ea |
string | Effect allele |
eaFreq |
number | Effect allele frequency |
pvalue |
number | Single variant p-value |
getAltFreqForPosition(position) → {number}
Return the alternate allele frequency for a variant
Parameters:
| Name | Type | Description |
|---|---|---|
position |
Variant position |
Returns:
Alt allele frequency
- Type
- number
getAltFreqForVariant(variant) → {number}
Return the alternate allele frequency for a variant
Parameters:
| Name | Type | Description |
|---|---|---|
variant |
Returns:
Alt allele frequency
- Type
- number
getVariantAtPosition(position)
Retrieve the variant at a given position.
Parameters:
| Name | Type | Description |
|---|---|---|
position |
Variant position |
subsetToVariants(variantList) → {ScoreStatTable}
Subset the score stats down to a subset of variants, in this exact ordering
Parameters:
| Name | Type | Description |
|---|---|---|
variantList |
List of variants |
Returns:
Score statistics after subsetting (not in-place, returns a new copy)
- Type
- ScoreStatTable