Denovo Gene Sets Section

The configuration section for denovo gene sets follows the general INI format. Its name must be denovoGeneSets - this will indicate that it is a denovo gene sets configuration section. This configuration section must properly describe one or more denovo gene sets for one study. This is an optional section.

Example Configuration

[denovoGeneSets]
enabled = yes

peopleGroups = status

standardCriterias.effect_types.segments=LGDs:LGDs,Missense:missense,Synonymous:synonymous
standardCriterias.sexes.segments=Female:F,Male:M,Unspecified:U

recurrencyCriteria.segments=Single:1:2,Triple:3:-1,Recurrent:2:-1

geneSetsNames=LGDs,LGDs.Male,LGDs.Female,LGDs.Recurrent,LGDs.Single,LGDs.Triple,
    Missense,Missense.Male,Missense.Female,Missense.Recurrent,Missense.Triple,
    Synonymous,Synonymous.Male,Synonymous.Female,Synonymous.Recurrent,Synonymous.Triple

[denovoGeneSets]

The properties for this section are explained below.

peopleGroups

peopleGroups = <comma-separated list of people groups>

peopleGroups is a comma-separated list of ids of people groups (defined in the People Group Section section in the study config), indicating which people groups to generate denovo gene sets for.

standardCriterias.<standard criteria id>.segments

standardCriterias.<standard criteria id>.segments = <<<standard criteria name 1>:<standard criteria value 1>>,<<standard criteria name 2>:<standard criteria value 2>>,<...>>

This property defines standard criteria segments indicating a group of genes and their families. The configured standard criterias can be combined together, or with recurrencyCriteria, in the geneSetsNames property in this section. The combinations will then be added as groups of denovo gene sets (which will be available in the Gene Sets filter in the Genotype Browser of the study).

Elements of the standard criteria segments are:

<standard criteria id> indicates the id of the standard criteria. The id must be one of the defined filters by which you can query variants in the backend. The possible filters are defined here.

<standard criteria name> indicates the display name of the group defined by this standard criteria.

<standard criteria value> indicates the value used when querying variants for the denovo gene set group defined by this standard criteria.

recurrencyCriteria.segments

recurrencyCriteria.segments = <>

geneSetsNames

geneSetsNames = <<<standard or recurrency criteria 1>.<standard or recurrency criteria 2>.<...>>,<...>>

The names of denovo gene set combinations which are defined by combining standardCriterias and/or recurrencyCriteria. This name represents the configuration of the denovo gene set. All combinations listed here will be available in the Gene Sets filter in the Genotype Browser of the study.

enabled

enabled = <boolean>

DEFAULT: True

This property enables the denovo gene sets functionality for the study. This property takes a boolean value.