collapseExpData: Combine multiple data sets
In Genominator: Analyze, manage and store genomic data

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

This function takes a dataset with data from multiple experiments, and combines the data across multiple experiments according to a user-specified function.

collapseExpData(expData, tablename = NULL,
  what = getColnames(expData, all = FALSE), groups = "COL",
  collapse = c("sum", "avg", "weighted.avg"), overwrite = FALSE,
  deleteOriginal = FALSE, verbose = getOption("verbose"))

`expData`	An object of class `ExpData`.
`tablename`	Name of database table to write output data to.
`what`	Data columns to apply `collapse` function to.
`groups`	Vector of length `what` indicating how columns should be grouped when applying `collapse` function.
`collapse`	Function to apply to grouped columns.
`overwrite`	Logical indicating whether database referred to in `tablename` argument should be overwritten.
`deleteOriginal`	Logical indicating whether original database in `ExpData` object should be deleted.
`verbose`	Logical indicating whether details should be printed.

This function can be thought of as similar to tapply, operating over the entries in the data set, applying the function specified in the collapse argument, grouping the data as indicated in the groups argument.

Returns an object of class ExpData.

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

See Genominator vignette for more information.

ed <- ExpData(system.file(package = "Genominator", "sample.db"),
              tablename = "raw")
nd <- importToExpData(head(ed, -1), dbFilename = tempfile(),
                      tablename = "collapsed")
head(nd)
cd <- collapseExpData(nd, tablename = "bio", overwrite = TRUE,
                      groups = c("mut", "mut", "wt", "wt"))
                      
head(cd)