read multiple rrbs bed files

read.bed.files.rrbs.R

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
## --------------
##               id  chr     start       end strand coverage numCs numTs
## 1 chr1.100002990 chr1 100002990 100002990      +        3     1     2
## 2 chr1.100003154 chr1 100003154 100003154      -       19     1    18
## 3   chr1.1000171 chr1   1000171   1000171      +       26     7    19
## 4   chr1.1000191 chr1   1000191   1000191      +       26    14    12
## 5   chr1.1000192 chr1   1000192   1000192      -       22     9    13
## 6   chr1.1000199 chr1   1000199   1000199      +       26    15    11
## --------------
## sample.id: test 
## assembly: hg19 
## context: CpG 
## resolution: base 
## 
## methylRaw object with 1233588 rows
## --------------
##             id  chr   start     end strand coverage numCs numTs
## 1 chr1.1000171 chr1 1000171 1000171      +       22     1    21
## 2 chr1.1000191 chr1 1000191 1000191      +       22     4    18
## 3 chr1.1000192 chr1 1000192 1000192      -       12     4     8
## 4 chr1.1000199 chr1 1000199 1000199      +       22    11    11
## 5 chr1.1000200 chr1 1000200 1000200      -       12     4     8
## 6 chr1.1000207 chr1 1000207 1000207      -       12     4     8
## --------------
## sample.id: control 
## assembly: hg19 
## context: CpG 
## resolution: base 
## 
## treament: 1 0