read.csv.sql: Main workhorse of makeDb

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

Description

Edited version of read.csv.sql in the sqldf package (tcltk functionality removed), used mainly to create a SQLite database from a text file. The function makeDb wraps this function in the tornado package, so no need to execute this directly.

Usage

read.csv.sql(file, sql = "select * from file", header = TRUE, sep = ",",
  row.names, eol, skip, filter, nrows, field.types, comment.char,
  dbname = tempfile(), drv = "SQLite", ...)

Arguments

file	A file path or a URL (beginning with http:// or ftp://). If the filter argument is used and no file is to be input to the filter then file can be omitted, NULL, NA or "". The textfile argument from makeDb is used here.
sql	character string holding an SQL statement. The table representing the file should be referred to as file.
header	as in read.csv
sep	as in read.csv
row.names	as in read.csv
eol	Character that ends lines
skip	Skip indicated number of lines in input file.
filter	see read.csv.sql in sqldf
nrows	Number of rows used to determine column types. It defaults to 50. Using -1 causes it to use all rows for determining column types. This argument is rarely needed.
field.types	A list whose names are the column names and whose contents are the SQLite types (not the R class names) of the columns. Specifying these types improves how fast it takes. Unless speed is very important this argument is not normally used.
comment.char	If specified this character and anything following it on any line of the input will be ignored.
dbname	As in sqldf except that the default is tempfile(). Specifying NULL will put the database in memory which may improve speed but will limit the size of the database by the available memory. When using tornado, tempfile() is not used: dbname must be provided as an argument to makeDb.
drv	ignored: the only drive used can be SQLite.
...	arguments passed to sqldf.

Details

This function is entirely wrapped by makeDb – experienced users may use this for debugging, but otherwise not usually necessary to call directly.

Value

If the sql statement is a select statement then a data frame is returned. In tornado, this is never the case.

References

http://cran.r-project.org/web/packages/sqldf/sqldf.pdf

See Also

makeDb

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