DMR id with Methylkit

Install should only have to occur once.

source("http://methylkit.googlecode.com/files/install.methylKit.R")

# installing the package with the dependencies
install.methylKit(ver="0.9.2",dependencies=TRUE)

library(methylKit)

library(data.table)

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 object is masked from 'package:stats':
## 
##     xtabs
## 
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, as.vector, cbind,
##     colnames, duplicated, eval, evalq, Filter, Find, get,
##     intersect, is.unsorted, lapply, Map, mapply, match, mget,
##     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
##     rbind, Reduce, rep.int, rownames, sapply, setdiff, sort,
##     table, tapply, union, unique, unlist
## 
## Loading required package: IRanges
## Loading required package: XVector
## 
## Attaching package: 'GenomicRanges'
## 
## The following object is masked from 'package:data.table':
## 
##     last

file.list <- list('/Volumes/web/cnidarian/YE_control_22sm_methkit.txt','/Volumes/web/cnidarian/YE_mix_22sm_methkit.txt')

myobj=read(file.list,sample.id=list("mix","control"),assembly="ensembl",treatment=c(1,0))

meth<-unite(myobj)

## Error: Join results in 24343272 rows; more than 5380020 =
## max(nrow(x),nrow(i)). Check for duplicate key values in i, each of which
## join to the same group in x over and over again. If that's ok, try
## including `j` and dropping `by` (by-without-by) so that j runs for each
## group to avoid the large allocation. If you are sure you wish to proceed,
## rerun with allow.cartesian=TRUE. Otherwise, please search for this error
## message in the FAQ, Wiki, Stack Overflow and datatable-help for advice.

nrow(meth)

## Error: error in evaluating the argument 'x' in selecting a method for function 'nrow': Error: object 'meth' not found