Calculates pairwise Pearson correlations between provided MEDIPS SETs

Description

The function calculates genome wide Pearson correlations between all pairs of provided MEDIPS SETs.

Usage

MEDIPS.correlation(MSets=NULL, plot = T, method="spearman")

Arguments

Value

a correlation matrix

Author(s)

Lukas Chavez

Examples

library(MEDIPSData)
data(hESCs_MeDIP)
data(DE_MeDIP)

correlation = MEDIPS.correlation(MSets=c(hESCs_MeDIP[[1]], DE_MeDIP[[1]]), plot = FALSE)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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'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(MEDIPS)
Loading required package: BSgenome
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
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MEDIPS/MEDIPS.correlation.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MEDIPS.correlation
> ### Title: Calculates pairwise Pearson correlations between provided MEDIPS
> ###   SETs
> ### Aliases: MEDIPS.correlation
> 
> ### ** Examples
> 
> 
> library(MEDIPSData)
> data(hESCs_MeDIP)
> data(DE_MeDIP)
> 
> correlation = MEDIPS.correlation(MSets=c(hESCs_MeDIP[[1]], DE_MeDIP[[1]]), plot = FALSE)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>