source("/Volumes/web/bivalvia/course materials/biostats.R")
library(methylKit)
install.packages("data.table")
source("http://www.bioconductor.org/biocLite.R")
biocLite("GenomicRanges")
library(data.table)
library(GenomicRanges)
file.list <- list("BiGill_v9_A_MethylKit.csv", "MethylKit_BiGO.csv")
myobj<-read( file.list,pipeline=list(fraction=TRUE,chr.col=1,start.col=2,end.col=2,
coverage.col=4,strand.col=3,freqC.col=5 ),
sample.id=list("gill","gonad"),assembly="v9",treatment=c(1,0))
file.list <- list("BiGill_v9_A_MethylKit.csv", "MethylKit_BiGO.csv")
myobj<-read( file.list,pipeline=list(fraction=TRUE,chr.col=1,start.col=2,end.col=2,
coverage.col=4,strand.col=3,freqC.col=5 ),
sample.id=list("gill","gonad"),assembly="v9",treatment=c(1,0))
library(methylKit)
library(methylKit)
install.packages("data.table")
source("http://www.bioconductor.org/biocLite.R")
biocLite("GenomicRanges")
library(data.table)
library(GenomicRanges)
file.list <- list("BiGill_v9_A_MethylKit.csv", "MethylKit_BiGO.csv")
myobj<-read( file.list,pipeline=list(fraction=TRUE,chr.col=1,start.col=2,end.col=2,
myobj<-read( file.list,pipeline=list(fraction=TRUE,chr.col=1,start.col=2,end.col=2,
myobj<-read( file.list,pipeline=list(fraction=TRUE,chr.col=1,start.col=2,end.col=2,
coverage.col=4,strand.col=3,freqC.col=5 ),
sample.id=list("gill","gonad"),assembly="v9",treatment=c(1,0))
file.list <- list("BiGill_v9_A_MethylKit.csv", "MethylKit_BiGO.csv") #
myobj<-read( file.list,pipeline=list(fraction=TRUE,chr.col=1,start.col=2,end.col=2,#
coverage.col=4,strand.col=3,freqC.col=5 ),#
sample.id=list("gill","gonad"),assembly="v9",treatment=c(1,0))
file.list
myobj<-read( file.list,pipeline=list(fraction=TRUE,chr.col=1,start.col=2,end.col=2,
coverage.col=4,strand.col=3,freqC.col=5 ),
sample.id=list("gill","gonad"),assembly="v9",treatment=c(1,0))
getMethylationStats(myobj[[1]],plot=F,both.strands=F)
getMethylationStats(myobj[[1]],plot=F,both.strands=F)