Reorder all elements of a ScoreMatrixList to a given ordering vector

Description

Reorder all elements of a ScoreMatrixList to a given ordering vector

Usage

orderBy(sml, ord.vec)

## S4 method for signature 'ScoreMatrixList'
orderBy(sml, ord.vec)

Arguments

Value

ScoreMatrixList object

Examples

library(GenomicRanges)
data(cage)
data(cpgi)
data(promoters)

cage$tpm = NULL
targets = GRangesList(cage=cage, cpgi=cpgi)
sml = ScoreMatrixList(targets, promoters, bin.num=10)
kmeans.clust = kmeans(sml$cage,3)

sml.ordered = orderBy(sml, kmeans.clust$cluster)

multiHeatMatrix(sml.ordered)

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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> library(genomation)
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genomation/orderBy-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: orderBy
> ### Title: Reorder all elements of a ScoreMatrixList to a given ordering
> ###   vector
> ### Aliases: orderBy orderBy,ScoreMatrixList-method
> 
> ### ** Examples
> 
> library(GenomicRanges)
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

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: GenomeInfoDb
> data(cage)
> data(cpgi)
> data(promoters)
> 
> cage$tpm = NULL
> targets = GRangesList(cage=cage, cpgi=cpgi)
> sml = ScoreMatrixList(targets, promoters, bin.num=10)
working on cage
working on cpgi
> kmeans.clust = kmeans(sml$cage,3)
> 
> sml.ordered = orderBy(sml, kmeans.clust$cluster)
> ## No test: 
> multiHeatMatrix(sml.ordered)
> ## End(No test)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>