gemini_query_wrapper: GEMINI query wrapper

In davemcg/SeeGEM: Integrate 'GEMINI' (and 'peddy') Output into Interactive Html Document

Description

A barebones GEMINI wrapper which passes on your GEMINI command to 'gemini query –header -q' on the command line. I imagine this will mostly be used for users with already functional 'gemini query –header -q' commands. You must escape (append \) your quote marks.

Usage

gemini_query_wrapper(gemini_db, test_name = "CUSTOM1", output = NA,
  ...)

Arguments

gemini_db	is the name of your GEMINI database (with path, if necessary)
test_name	The identifying name given to your query. Will be used in the interative document to filter query/GEMINI sub command types
output	By default the data frame will be returned. If you give path/name.tsv a tab separate file will be written
...	Your GEMINI command, past 'gemini query -q'

Value

None

Examples

## Not run: 
gemini_query_wrapper('/path/to/your/gemini.db', ... = "\"SELECT * FROM 
variants WHERE (aaf_esp_all < 0.01 AND IMPACT_SO LIKE '%STOP%' AND 
filter is NULL) LIMIT 20\"")

## End(Not run)

davemcg/SeeGEM documentation built on May 5, 2019, 1:34 a.m.