merge: Merge RGList\_CALIB or SpikeList objects

In CALIB: Calibration model for estimating absolute expression levels from microarray data

Description

Merge two RGList_CALIB objects or two SpikeList objects in possibly irregular order.

Usage

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

Arguments

x	an RGList_CALIB object or an SpikeList object.
y	corresponding RGList_CALIB object or SpikeList object. Has the same genes or spikes as x, possibly in a different order,but with different arrays.
...	other arguments can be used in merge in the base packge.

Details

RGList_CALIB and SpikeList

objects are list objects containing numeric matrices with the same dimensions. The RGLists\_CALIB or SpikeLists 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$R is matched with the first occurrence of the same name in y$R, the second with the second, and so on. The final vector of row names is the same as in x.

Value

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

Note

If the RGList_CALIB or SpikeList objects contain the same number of genes or spikes in the same order then the appropriate function to combine them is cbind rather than merge.

Author(s)

Hui Zhao

References

merge in limma package

See Also

merge in the base package

merge in the limma package

Examples

R1 <- G1 <- matrix(1:8,4,2)
rownames(R1) <- rownames(G1) <- c("g1","g1","g2","g3")
colnames(R1) <- colnames(G1) <- c("a1","a2")
RG1 <- new("RGList_CALIB",list(R=R1,G=G1))

R2 <- G2 <- matrix(9:16,4,2)
rownames(R2) <- rownames(G2) <- c("g2","g3","g1","g1")
colnames(R2) <- colnames(G2) <- c("a3","a4")
RG2 <- new("RGList_CALIB",list(R=R2,G=G2))

RG12 <- merge(RG1,RG2)
RG21 <- merge(RG2,RG1)

CALIB documentation built on Oct. 31, 2019, 3:45 a.m.