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Last data update: 2014.03.03

R: Compute distances between Peaks

compDists

R Documentation

Compute distances between Peaks

Description

This function computes pairwise distances between histograms according to the dist.method (MMD, KS). For large data sets it is a bit time consuming.

Usage

compDists(MD, dist.method = "MMD", sigma = NULL, run.parallel = TRUE)

Arguments

`MD`	DBAmmd Object. This Object can be created using `DBAmmd()`.
`dist.method`	specify method used for distances between samples. Currently only Maximum Mean Discrepancy (MMD) and Kolmogorov-Smirnov (KS) implemented. (DEFAULT: 'MMD')
`sigma`	sigma parameter of the RBF kernel, determining the distance (along the genome) at which fragment counts decorrelate. If set to NULL, 100 random Peaks are used to determine sigma heuristically according to the method described in the MMDiff paper [1]. (DEFUALT: NULL)
`run.parallel`	whether to run in parallel (currently no parallelization implemented) (DEFAULT: FALSE)

Value

DBAmmd object with updated slot Dists

Author(s)

Gabriele Schweikert G.Schweikert@ed.ac.uk

References

[1] Schweikert et al. BMC Genomics 2013 ...

Examples


## Example using a small data set provided with this package:

data("MMD")
MMD.1 <- compDists(MMD)

# To inspect the computed distances:
D <- Dists(MMD.1,dist.method='MMD')
head(D)

# To analyse the result:
plotDists(MMD.1)

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 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MMDiff2)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Biobase
Welcome to Bioconductor

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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MMDiff2/compDists.Rd_%03d_medium.png", width=480, height=480)
> ### Name: compDists
> ### Title: Compute distances between Peaks
> ### Aliases: compDists
> 
> ### ** Examples
> 
> 
> ## Example using a small data set provided with this package:
> 
> data("MMD")
> MMD.1 <- compDists(MMD)
checking parameters...
estimating sigma...
pre-computing Kernel matrix...
computing 3 pair-wise distances...
computing distances for WT.AB2 vs Null.AB2
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