Combine multiple data sets

Description

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

Usage

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

Arguments

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.

Details

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.

Value

Returns an object of class ExpData.

Author(s)

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

See Also

See Genominator vignette for more information.

Examples

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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)