al2na

library(methylKit)

obj=read("bsmap_output.txt",sample.id="test",assembly="mm9",header=TRUE, context="CpG", resolution="base",
          pipeline=list(fraction=TRUE,chr.col=1,start.col=2,end.col=2,
                        coverage.col=6,strand.col=3,freqC.col=5 )
        )

obj

al2na

library(sqldf)
library(doBy)
library(plyr)
library(data.table)
 
n<-100000
grp1<-sample(1:750, n, replace=T)
grp2<-sample(1:750, n, replace=T)
d<-data.frame(x=rnorm(n), y=rnorm(n), grp1=grp1, grp2=grp2, n,
replace=T)

al2na

library(methylKit)
obj = read("wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep1.bed.gz",
                 sample.id = "test", assembly = "hg19", header = FALSE, 
                 context = "CpG", resolution = "base", 
                 pipeline = list(fraction = FALSE, chr.col = 1, start.col = 3, 
                                  end.col = 3,coverage.col = 5, strand.col = 6, 
                                  freqC.col = 11))

al2na

file.list = list("wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep1.bed.gz", 
                 "wgEncodeHaibMethylRrbsAg04449UwstamgrowprotSitesRep1.bed9.gz")
obj = read(file.list, sample.id = list("test", "control"), treatment = c(1,0), 
           assembly = "hg19", header = FALSE, context = "CpG", resolution = "base", 
           pipeline = list(fraction = FALSE, chr.col = 1, start.col = 3, end.col = 3, 
                          coverage.col = 5, strand.col = 6, freqC.col = 11))
obj
## methylRawList object with 2 methylRaw objects
## 
## methylRaw object with 1464031 rows

al2na

Here is how you can make a table in GFM format using knitr + ascii

render_gfm()
gfm_table <- function(x, ...) {
    require(ascii)
    y <- capture.output(print(ascii(x, ...), type = "org"))
 # substitute + with | for table markup

al2na

.libPaths("/work2/gschub/altuna/RlibsDev")
require(data.table)

summarizeScores<-function(loc.gr,score.gr,score.col){

  ov <- as.matrix(findOverlaps(loc.gr,score.gr))
  
  dt=data.table(id=ov[,1],score=values(score.gr)[ov[,2],which(names(values(score.gr))==score.col)])
  dt=dt[,list(av=mean(score)),by=id]
  

al2na

  require(data.table)
  require(QuasR)
 
# arguments:  
# proj: qProject object
# range: GRanges object with ONE!!!! range
# samp: sample.name
#
getCMethMatrix<-function(proj,range,samp){  
  Cs=qMeth(proj, query=range,mode="allC",reportLevel="alignment")

al2na

setGeneric("tileMethylCounts2", 
           function(object,win.size=1000,step.size=1000,cov.bases=0)
             standardGeneric("tileMethylCounts2") )

setMethod("tileMethylCounts2", signature(object="methylRaw"),
          function(object,win.size,step.size,cov.bases){
            
            g.meth =as(object,"GRanges")
            chrs   =as.character(unique(seqnames(g.meth)))
            widths =seqlengths(g.meth)

al2na

#' call primer3 for a given set of DNAstringSet object
#'
#' @param seq DNAstring object, one DNA string for the given amplicon
#' @param size_range default: '151-500'
#' @param Tm melting temprature parameters default:c(55,57,58)
#' @param name name of the amplicon in chr_start_end format
#' @param primer3 primer3 location
#' @param therme.param thermodynamic parameters folder
#' @param settings text file for parameters
#' @author Altuna Akalin modified Arnaud Krebs' original function

al2na

require(GenomicRanges)
require(Biostrings)


#' get OE ratio and GC content for a given set of DNAstrings
getOE.strset<-function(str.set)
{
  di.mat=dinucleotideFrequency(  str.set )
  a.mat =alphabetFrequency( str.set ,baseOnly=TRUE )
  exp=(a.mat[,2]*a.mat[,3])/width(str.set )