Description Usage Arguments Value Details Examples
The function summarizes methylated/unmethylated base counts over tilling windows accross genome. This function can be used when differential methylated analysis is preferable to tilling windows instead of base pairs.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25  tileMethylCounts(object,win.size=1000,step.size=1000,cov.bases=0,mc.cores=1,save.db,...)
## S4 method for signature 'methylRaw'
tileMethylCounts(object, win.size = 1000,
step.size = 1000, cov.bases = 0, mc.cores = 1, save.db = FALSE, ...)
## S4 method for signature 'methylRawList'
tileMethylCounts(object, win.size = 1000,
step.size = 1000, cov.bases = 0, mc.cores = 1, save.db = FALSE, ...)
## S4 method for signature 'methylBase'
tileMethylCounts(object, win.size = 1000,
step.size = 1000, cov.bases = 0, mc.cores = 1, save.db = FALSE, ...)
## S4 method for signature 'methylRawDB'
tileMethylCounts(object, win.size = 1000,
step.size = 1000, cov.bases = 0, mc.cores = 1, save.db = TRUE, ...)
## S4 method for signature 'methylRawListDB'
tileMethylCounts(object, win.size = 1000,
step.size = 1000, cov.bases = 0, mc.cores = 1, save.db = TRUE, ...)
## S4 method for signature 'methylBaseDB'
tileMethylCounts(object, win.size = 1000,
step.size = 1000, cov.bases = 0, mc.cores = 1, save.db = TRUE, ...)

object 

win.size 
an integer for the size of the tiling windows 
step.size 
an integer for the step size of tiling windows 
cov.bases 
minimum number of bases to be covered in a given window 
mc.cores 
number of cores to use when processing 
save.db 
A Logical to decide whether the resulting object should be saved as flat file database or not, default: explained in Details sections 
... 
optional Arguments used when save.db is TRUE

methylRaw
,methylBase
or methylRawList
object
The parameter chunk.size
is only used when working with
methylRawDB
, methylBaseDB
or methylRawListDB
objects,
as they are read in chunk by chunk to enable processing largesized objects
which are stored as flat file database.
Per default the chunk.size is set to 1M rows, which should work for most
systems. If you encounter memory problems or
have a high amount of memory available feel free to adjust the chunk.size
.
The parameter save.db
is per default TRUE for methylDB objects as
methylRawDB
, methylBaseDB
or methylRawListDB
,
while being per default FALSE for methylRaw
, methylBase
or
methylRawList
. If you wish to save the result of an
inmemorycalculation as flat file database or if the size of the database
allows the calculation inmemory,
then you might want to change the value of this parameter.
1 2 3 4  data(methylKit)
tiled.methylRaw=tileMethylCounts(object=methylRawList.obj,win.size=1000,
step.size=1000,cov.bases=0)

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