Make a matrix suitable for use with RUVSeq methods such as RUVs.

Description

Each row in the returned matrix corresponds to a set of replicate samples. The number of columns is the size of the largest set of replicates; rows for smaller sets are padded with -1 values.

Usage

makeGroups(xs)

Arguments

Author(s)

Kamil Slowikowski

See Also

RUVs

Examples

makeGroups(c("A","B","B","C","C","D","D","D","A"))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(RUVSeq)
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: EDASeq
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: edgeR
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RUVSeq/makeGroups.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeGroups
> ### Title: Make a matrix suitable for use with RUVSeq methods such as
> ###   'RUVs'.
> ### Aliases: makeGroups
> 
> ### ** Examples
> 
> makeGroups(c("A","B","B","C","C","D","D","D","A"))
     [,1] [,2] [,3]
[1,]    1    9   -1
[2,]    2    3   -1
[3,]    4    5   -1
[4,]    6    7    8
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>