class DGV extends CNVDatabase
A CNVDatabase implementation for CNVs from the Database of Genomic Variants (sourced via UCSC).
Note: the database is not parsed by the constructor, you must call the parse() method yourself before using any query methods.
| Type | Name and description |
|---|---|
static java.util.List<java.lang.String> |
DGV_COLUMNSColumns from schema of DGV in UCSC table |
RangedData |
dgv |
java.lang.String |
dgvFile |
| Constructor and description |
|---|
DGV
(java.lang.String dgvFile) |
DGV
(RangedData dgv) |
| Type Params | Return Type | Name and description |
|---|---|---|
|
java.util.List<gngs.Region> |
filterByType(java.lang.String type, java.util.List<gngs.Region> regions) |
|
double |
maxFreq(java.util.Map options, gngs.Region region)Find the maximum frequency of this CNV within any study within DGV where the study has more than a minimum threshold size (default: 10 people). |
|
DGV |
parse()Parse the data source set for this database |
|
java.util.List<gngs.Region> |
queryOverlapping(gngs.Region r)return CNVS overlapping the specified region |
| Methods inherited from class | Name |
|---|---|
class CNVDatabase |
maxFreq, queryOverlapping |
Columns from schema of DGV in UCSC table
Find the maximum frequency of this CNV within any study within DGV where the study has more than a minimum threshold size (default: 10 people).
region - region to searchParse the data source set for this database
return CNVS overlapping the specified region @return
Groovy Documentation