merge: Merge RGList or MAList Data Objects

In limma: Linear Models for Microarray Data

Description

Merge two microarray data sets represented by RGLists in possibly irregular order.

Usage

## S3 method for class 'RGList'
merge(x,y,...)

Arguments

x	data object of class RGList, MAList, EList or EListRaw.
y	data object of same class as x, corresponding to the same genes as for x, possibly in a different order, but with different arrays.
...	other arguments are accepted but not used at present

Details

RGList, MAList, EListRaw and EList data objects are lists containing numeric matrices all of the same dimensions. The data objects are merged by merging each of the components by row names or, if there are no row names, by IDs in the genes component. Unlike when using cbind, row names are not required to be in the same order or to be unique. In the case of repeated row names, the order of the rows with repeated names in preserved. This means that the first occurrence of each name in x is matched with the first occurrence of the same name in y, the second with the second, and so on. The final vector of row names is the same as in x.

Note: if the objects contain the same number of genes in the same order then the appropriate function to combine them is cbind rather than merge.

Value

An merged object of the same class as x and y with the same components as x. Component matrices have the same rows names as in x but columns from y as well as from x.

Author(s)

Gordon Smyth

See Also

R base provides a merge method for merging data.frames.

An overview of limma commands for reading, subsetting and merging data is given in 03.ReadingData.

Examples

M <- A <- matrix(11:14,4,2)
rownames(M) <- rownames(A) <- c("a","a","b","c")
MA1 <- new("MAList",list(M=M,A=A))

M <- A <- matrix(21:24,4,2)
rownames(M) <- rownames(A) <- c("b","a","a","c")
MA2 <- new("MAList",list(M=M,A=A))

merge(MA1,MA2)
merge(MA2,MA1)

Example output

An object of class "MAList"
$M
  [,1] [,2] [,3] [,4]
a   11   11   22   22
a   12   12   23   23
b   13   13   21   21
c   14   14   24   24

$A
  [,1] [,2] [,3] [,4]
a   11   11   22   22
a   12   12   23   23
b   13   13   21   21
c   14   14   24   24

An object of class "MAList"
$M
  [,1] [,2] [,3] [,4]
b   21   21   13   13
a   22   22   11   11
a   23   23   12   12
c   24   24   14   14

$A
  [,1] [,2] [,3] [,4]
b   21   21   13   13
a   22   22   11   11
a   23   23   12   12
c   24   24   14   14

limma documentation built on Nov. 8, 2020, 8:28 p.m.