methylKit：差异甲基化分析

1. 1Methylation输入格式

coverage：覆盖这个位点的reads数目。
freqC：甲基化C的比例
freqT：非甲基化C的比例

1.2 纯文本的读取：methRead

file.list是一个列表，里面的元素是每个文件名
myobj = methRead(file.list,
			   	 assembly = "hg19",
			   	 sample.id = list("test1","test2","ctrl1","ctrl2"),
			   	 treatment = c(1,1,0,0),
			   	 context = "CpG"
			   	 )
treatment指定样本的分组，1是treatment组，0是control组；assembly指定组装版本。

1.3 bam文件读取：processBismarkAln

bam.list是一个列表，里面元素是每个bam文件名。
myobj = processBismarkAln(bam.list,
						  sample.id = c("sample_A1","sample_A2","sample_B1","sample_B2"),
						  assembly = "hg19",