class DecipherCNVs extends CNVDatabase
A CNVDatabase implementation for CNVs from Decipher Developmental Delay project.
Note: the database is not parsed by the constructor, you must call the parse() method yourself before using any query methods.
See https://decipher.sanger.ac.uk/files/downloads/population_cnv.txt.gz
| Type | Name and description |
|---|---|
static java.util.List<java.lang.String> |
DECIPHER_COLUMNSColumns from schema of DGV in UCSC table |
RangedData |
ddd |
java.lang.String |
dddFile |
| Constructor and description |
|---|
DecipherCNVs
(java.lang.String dddFile) |
DecipherCNVs
(RangedData ddd) |
| Type Params | Return Type | Name and description |
|---|---|---|
|
double |
maxFreq(java.util.Map options, gngs.Region region)Find the maximum frequency of this CNV within any study within DDD where the study has more than a minimum threshold size (default: 10 people). |
|
DecipherCNVs |
parse() |
|
java.util.List<gngs.Region> |
queryOverlapping(gngs.Region r)Convenience method to 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 DDD where the study has more than a minimum threshold size (default: 10 people).
region - region to searchConvenience method to return CNVS overlapping the specified region @return
Groovy Documentation