Combine a list of RTCA objects

Description

Combine a list of RTCA objects

Usage

combineRTCA(list)

Arguments

Details

The current implementation requires all the objects have exactly the same time-points recorded (or at least of same length).

The combined RTCA object has an obligatory column in the phenoData ‘Plate’ (upper-case!), which matches the names of the RTCA list. When the list has no names, the ‘Plate’ field is filled with integer index starting from 1.

Value

A new RTCA object

Note

Special attention should be given to the cases where the list parameter partially has names. In this case all items without name will be assigned to a ‘Plate’ field of empty string (“”). Therefore it is advised either to assign names to all items of the list, or leave them all off.

Author(s)

Jitao David Zhang jitao_david.zhang@roche.com

Examples

## An artificial example
require(RTCA)
  
ofile <- system.file("/extdata/testOutput.csv", package="RTCA")
x <- parseRTCA(ofile)

xSub1 <- x[,1:3]
xSub2 <- x[,4:ncol(x)]
xComb <- combineRTCA(list(sub1=xSub1, sub2=xSub2))
identical(exprs(x), exprs(xComb))
pData(xComb)$Plate

## in case of nameless list
pData(combineRTCA(list(xSub1, xSub2)))$Plate

## partial names
pData(combineRTCA(list(a=xSub1, xSub2)))$Plate

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(RTCA)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: gtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RTCA/combineRTCA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: combineRTCA
> ### Title: Combine a list of RTCA objects
> ### Aliases: combineRTCA
> 
> ### ** Examples
> 
> ## An artificial example
> require(RTCA)
>   
> ofile <- system.file("/extdata/testOutput.csv", package="RTCA")
> x <- parseRTCA(ofile)
Read 245 items
> 
> xSub1 <- x[,1:3]
> xSub2 <- x[,4:ncol(x)]
> xComb <- combineRTCA(list(sub1=xSub1, sub2=xSub2))
> identical(exprs(x), exprs(xComb))
[1] TRUE
> pData(xComb)$Plate
 [1] sub1 sub1 sub1 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2
[16] sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2
[31] sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2
[46] sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2
[61] sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2
[76] sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2 sub2
[91] sub2 sub2 sub2 sub2 sub2 sub2
Levels: sub1 sub2
> 
> ## in case of nameless list
> pData(combineRTCA(list(xSub1, xSub2)))$Plate
 [1] 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[39] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[77] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
Levels: 1 2
> 
> ## partial names
> pData(combineRTCA(list(a=xSub1, xSub2)))$Plate
 [1] a a a                                                                      
[39]                                                                            
[77]                                        
Levels:  a
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>