combine {Biobase} | R Documentation

## Methods for Function combine in Package ‘Biobase’

### Description

This generic function handles methods for combining or merging different Bioconductor data structures. It should, given an arbitrary number of arguments of the same class (possibly by inheritance), combine them into a single instance in a sensible way (some methods may only combine 2 objects, ignoring `...` in the argument list; because Bioconductor data structures are complicated, check carefully that `combine` does as you intend).

### Usage

    combine(x, y, ...)

### Arguments

`x` | One of the values.
`y` | A second value.
`...` | Any other objects of the same class as `x` and `y`.

### Details

There are two basic combine strategies. One is an intersection strategy. The returned value should only have rows (or columns) that are found in all input data objects. The union strategy says that the return value will have all rows (or columns) found in any one of the input data objects (in which case some indication of what to use for missing values will need to be provided).

These functions and methods are currently under construction. Please let us know if there are features that you require.

### Value

A single value of the same class as the most specific common ancestor (in class terms) of the input values. This will contain the appropriate combination of the data in the input values.

### Methods

`combine(x=ANY, missing)`
  Return the first (x) argument unchanged.
`combine(data.frame, data.frame)`
  Combines two `data.frame` objects so that the resulting `data.frame` contains all rows and columns of the original objects. Rows and columns in the returned value are unique, that is, a row or column represented in both arguments is represented only once in the result. To perform this operation, `combine` makes sure that data in shared rows and columns are identical in the two data.frames. Data differences in shared rows and columns usually cause an error. `combine` issues a warning when a column is a `factor` and the levels of the factor in the two data.frames are different.
`combine(matrix, matrix)`
  Combined two `matrix` objects so that the resulting `matrix` contains all rows and columns of the original objects. Both matricies must have `dimnames`. Rows and columns in the returned value are unique, that is, a row or column represented in both arguments is reprensted only once in the result. To perform this operation, `combine` makes sure that data in shared rows and columns are all equal in the two matricies.

Additional `combine` methods are defined for `AnnotatedDataFrame`, `AssayData`, `MIAME`, and `eSet` classes and subclasses.

### Author(s)

Biocore

### See Also

`merge`

### Examples

      x <- data.frame(x=1:5,
              y=factor(letters[1:5], levels=letters[1:8]),
              row.names=letters[1:5])
      y <- data.frame(z=3:7,
              y=factor(letters[3:7], levels=letters[1:8]),
              row.names=letters[3:7])
      combine(x,y)

      w <- data.frame(w=4:8,
             y=factor(letters[4:8], levels=letters[1:8]),
             row.names=letters[4:8])
      combine(w, x, y)

      # y is converted to 'factor' with different levels
      df1 <- data.frame(x=1:5,y=letters[1:5], row.names=letters[1:5])
      df2 <- data.frame(z=3:7,y=letters[3:7], row.names=letters[3:7])
      try(combine(df1, df2)) # fails
      # solution 1: ensure identical levels
      y1 <- factor(letters[1:5], levels=letters[1:7])
      y2 <- factor(letters[3:7], levels=letters[1:7])
      df1 <- data.frame(x=1:5,y=y1, row.names=letters[1:5])
      df2 <- data.frame(z=3:7,y=y2, row.names=letters[3:7])
      combine(df1, df2)
      # solution 2: force column to be 'character'
      df1 <- data.frame(x=1:5,y=I(letters[1:5]), row.names=letters[1:5])
      df2 <- data.frame(z=3:7,y=I(letters[3:7]), row.names=letters[3:7])
      combine(df1, df2)

      m <- matrix(1:20, nrow=5, dimnames=list(LETTERS[1:5], letters[1:4]))
      combine(m[1:3,], m[4:5,])
      combine(m[1:3, 1:3], m[3:5, 3:4]) # overlap

[Package Biobase version 2.2.2 Index]