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The function creates a new methylRawList, methylRawListDB,
methylBase or methylBaseDB
object by selecting a subset of samples from the input object, which is
a methylRawList or methylBase object. You can use the function
to partition a large methylRawList or methylBase object
to smaller object based on sample ids or when you want to reorder samples
and/or give a new treatmet vector.
reorganize(methylObj, sample.ids, treatment, chunk.size = 1e+06,
save.db = FALSE, ...)# S4 method for methylBase
reorganize(methylObj, sample.ids, treatment,
chunk.size = 1e+06, save.db = FALSE, ...)
# S4 method for methylRawList
reorganize(methylObj, sample.ids, treatment,
chunk.size = 1e+06, save.db = FALSE, ...)
# S4 method for methylRawListDB
reorganize(methylObj, sample.ids, treatment,
chunk.size = 1e+06, save.db = TRUE, ...)
# S4 method for methylBaseDB
reorganize(methylObj, sample.ids, treatment,
chunk.size = 1e+06, save.db = TRUE, ...)
a methylRawList, methylRawListDB,
methylBase or methylBaseDB object
a vector for sample.ids to be subset. Order is important and the order should be similar to treatment. sample.ids should be a subset or reordered version of sample ids in the input object.
treatment vector, should be same length as sample.ids vector
Number of rows to be taken as a chunk for processing the
methylBaseDB or methylRawListDB objects, default: 1e6
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
suffix
A character string to append to the name of the output
flat file database,
only used if save.db is true, default actions:
append “_filtered” to current filename
if database already exists or generate new file
with filename “sampleID_filtered”
dbdir
The directory where flat file database(s) should be
stored, defaults
to getwd(), working directory for newly stored databases
and to same directory for already existing database
dbtype
The type of the flat file database, currently only option
"tabix"
returns a methylRawList, methylRawListDB,
methylBase or methylBaseDB object depending on the input object
The parameter chunk.size is only used when working with
methylBaseDB or methylRawListDB objects,
as they are read in chunk by chunk to enable processing large-sized
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
methylBaseDB and methylRawListDB,
while being per default FALSE for methylBase and
methylRawList. If you wish to save the result of an
in-memory-calculation as flat file database or if the size of the
database allows the calculation in-memory,
then you might want to change the value of this parameter.
# NOT RUN {
# this is a list of example files, ships with the package
file.list=list( system.file("extdata", "test1.myCpG.txt", package = "methylKit"),
system.file("extdata", "test2.myCpG.txt", package = "methylKit"),
system.file("extdata", "control1.myCpG.txt", package = "methylKit"),
system.file("extdata", "control2.myCpG.txt", package = "methylKit") )
# read the files to a methylRawList object: myobj
myobj=methRead( file.list,
sample.id=list("test1","test2","ctrl1","ctrl2"),
assembly="hg18",pipeline="amp",treatment=c(1,1,0,0))
meth=unite(myobj,destrand=TRUE)
# get samples named "test1" and "ctrl2" from myobj and create a new methylRawList object
myobj2=reorganize(myobj,sample.ids=c("test1","ctrl2"),treatment=c(1,0) )
# # get samples named "test1" and "ctrl2" from meth and create a new methylBase object
meth2 =reorganize(meth,sample.ids=c("test1","ctrl2"),treatment=c(1,0) )
# }
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