makeDb: Create SQLite database from text file

In leekgroup/derfinder: Differential expression analysis of RNA-seq data at base-pair resolution

Description

Dumps the contents of a table (saved as a text file) into a SQLite database, performing some filtering along the way.

Usage

makeDb(dbfile, textfile, tablename, sep = "\t", cutoff = 5)

Arguments

dbfile	Character string giving the file name/location of the database to be created. Generally ends in .db.
textfile	The text file containing the table to be dumped into dbfile.
tablename	Character string containing name to give the table inside dbfile.
sep	The separator used in textfile. The tornado pipeline creates tab-separated text files, so "\t" is the default.
cutoff	Rows in textfile must have at least one entry (not counting the first column, which is assumed to hold genomic position) greater than cutoff to be included in dbfile.

Value

No return, but writes the file dbfile containing table tablename by filtering textfile according to cutoff.

Note

The workhorse of this function is a modified version of read.csv.sql, found in the sqldf package.

Author(s)

Alyssa Frazee

leekgroup/derfinder documentation built on May 20, 2019, 11:30 p.m.