Creating Sungear Files
- Sungear Data File
- Gene/Case Definition File
- Group Definition File
- Group Hierarchy File
- Element to Group File
- GeneLights File
General Information
There are four files that are required for Sungear to load a Sungear file. There is a file for defining the genes, the groups, how the groups are organized, and which groups have which elements.
Comments are allowed at the beginning of each file, but not afterwards, in the form of beginning bracket and end bracket.
Example :{ comments in here }
Delimiters are pipes and in some instances spaces. '|' and ' '.
Files can be named with any or no extension.
Sungear Data File
This file contains two parts, the header and the data. The header contains a list of anchor names and a name for the elements. The anchor names will be displayed on the sungear dialog within the application. Element identification should be unique.
gene example
baseball example
Gene/Case Definition File
This file contains element identification and any other information you wished to be displayed about the elements. The element identification should be unique and will be used by the Sungear Data File and the Elements To Groupings File.
Formal Definition
ElementID | [Any Information]
Examples
gene example
baseball example
Group Definition File
This file contains group names and any other information you wished displayed about the groups.
Formal Definition
GroupName | [Any Information]
Examples
gene example
baseball example
Group Hierarchy File
This file contains how the groups are organized in a hierarchy. This is done by giving the group name followed by a list of groups that are underneath. This file can be blank but must be provided.
Formal Definition
GroupName | [GroupName [GroupName]*]
Example
gene example
baseball example
Group to Element
This puts all elements into the appropriate group. Elements may be put into separate groups.
Formal Definition
Group Name | Z Score | [Element]*
Example
gene example
baseball example
GeneLights
A GeneLights file has a similar format to the Sungear file. It specifies a value
(e.g. log fold change in expression) for each element across a range of conditions,
or "NA" if the value is unknown. Generally the conditions will be the
same as the Sungear anchors, but this is not required. The GeneLights file will be
automatically recognized and loaded if it has the same name as the Sungear file
with the addition of a ".gl" suffix.
Example
gene example