Up: Component summary
Up: Component summary
Component
TPqueryRetrieve target prediction and target validated data from an SQLite database to annotate a list of miRNAs or a list of miRNA-target gene pairs.
| Version | 0.3 |
|---|---|
| Bundle | sequencing |
| Categories | Integration smallRNA |
| Authors | Katherine Icay (katherine.icay@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | sqldf |
| Source files | component.xml SQLiteDB_xref.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| refTable | CSV | Mandatory | Tab-delimited CSV file with headers and at least one column containing IDs matching SQLite database keys to reference. If input only contains miRNAs, be sure to have a reference value in the parameters. |
Outputs| Name | Type | Description |
|---|---|---|
| array | Array<CSV> | If a reference value is given, results from each non-reference table will be output in separate files. |
| annot | CSV | If no reference value is given, contents of input file plus additional columns from TPtables merged according to the specified keys. NOTE: this only works correctly if input refTable contains miRNA-target gene pairs AND pairedKeys contains at least two refKeys matching the column name of the miRNAs and the column name of their targets. If either one is missing, the component will merge all possible combinations of rows. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| TPdb | string | "" | Absolute path to SQLite database. If the database was made by createSQLiteDB, value here should match a value in the DB_Destination_Folder column of input DBlist. |
| TPtables | string | "" | Comma-separated list of SQLite database tables found in the TPdb database to query. Order is important to the merging of the data and affects pairedKeys. |
| pairedKeys | string | "" | Comma-separated list key column pairs to merge. Format should be "refKeys=TPkeys". When multiple TPtables are given, refKeys always represents a previous TPtables' keys. |
| reference | string | "" | Name of SQLite database table to be used to merge with refTable and each non-reference TPtable. It will output an array if specified. Otherwise, it will output a single merged file. |
Test cases| Test case | Parameters▼ | IN refTable |
OUT array |
OUT annot |
||
|---|---|---|---|---|---|---|
| case1 | properties | refTable | (missing) | annot | ||
|
TPdb=relations/TestDB2, |
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| case2 | properties | refTable | array | annot | ||
|
reference=mirbaseIDs, |
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