# NOT RUN {
# reading one bismark file:
my.file=system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit")
obj=processBismarkAln(my.file,"test",assembly="hg18",save.folder=NULL,
save.context="CpG",read.context="CpG")
# reading multiple files
file.list2=list(system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"),
system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"),
system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"),
system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"))
objs=processBismarkAln(location=file.list2
,sample.id=list("test1","test2","ctrl1","ctrl1"),assembly="hg18",
save.folder=NULL,save.context=NULL,read.context="CpG",
nolap=FALSE,mincov=10,minqual=20,phred64=FALSE,
treatment=c(1,1,0,0))
# }
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