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

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

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

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("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