aggregateExpData: Collapse data into unique entries
In Genominator: Analyze, manage and store genomic data

Description Usage Arguments Details Value Author(s) See Also Examples

Collapses data based on unique combinations of values in a set of columns, by default adding a column giving counts of data entries with a particular combination.

aggregateExpData(expData, by = getIndexColumns(expData),
  tablename = NULL, deleteOriginal = FALSE, overwrite = FALSE,
  verbose = getOption("verbose"), colname = "counts",
  aggregator = paste("count(", by[1], ")", sep = ""))

`expData`	An object of class `ExpData`.
`by`	Vector containing column names used to define unique entries.
`tablename`	Name of database table to write output data to.
`deleteOriginal`	Logical indicating whether original database table in `ExpData` object should be deleted.
`overwrite`	Logical indicating whether database table referred to in `tablename` argument should be overwritten.
`verbose`	Logical indicating whether details should be printed.
`colname`	Name of column for recording aggregation output (by default, `counts`).
`aggregator`	SQLite code used for aggregating. See `Details` for more information.

By default this function counts instances of data entries with a particular combination of the values in the set of columns indicated in the by argument. Other SQLite commands can be indicated using the aggregator argument.

Returns an ExpData object.

James Bullard bullard@berkeley.edu, Kasper Daniel Hansen khansen@jhsph.edu

See Genominator vignette for more information.

N  <- 10000 # the number of observations. 
df <- data.frame(chr = sample(1:16, size = N, replace = TRUE),
                 location = sample(1:1000, size = N, replace = TRUE),
                 strand = sample(c(1L,-1L), size = N, replace = TRUE))
eDataRaw <- aggregateExpData(importToExpData(df, dbFilename = tempfile(), 
                             tablename = "ex_tbl", overwrite = TRUE))