Up: Component summary Component

TPquery

Retrieve 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,
TPtables=mirbaseIDs,
pairedKeys=id\=miRB21

case2 properties refTable array annot

reference=mirbaseIDs,
TPdb=relations/TestDB2,
TPtables=mirtarbase,
pairedKeys=id\=miRB21,ID\=mirbID,entrezID\=entrezID


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