Reconstruct methylBase or methylBaseDB object based on a new methylation percentage matrix
The function reconstructs a new methylBase object from an input methylBase object and percent methylation matrix. Basically, it uses the read coverages in the input methylBase object and deduces new number of methylated Cs and unmethylated Cs based on the input percent methylation matrix. It is ideally to be used to reconstruct methylBase objects after batch correction on percent methylation values. The percent methylation matrix rows must match methylBase object rows in order ,and in addition column order (the order of samples) in input methylBase must match the order in percent methylation matrix.
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percent methylation matrix, row order and order of the samples same as the methylBase object
Number of rows to be taken as a chunk for processing the
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
object where methylation percentage matches
methMat and coverages matches input
chunk.size is only used when working with
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
save.db is per default TRUE for methylDB
while being per default FALSE for
methylBase. 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.
Batch effect correction (if any batch effect exists) is a tricky issue.
We provide some simple ways to deal with it
But if you can find other ways to correct for batch effects and want
a methylBase object with the corrected percent methylation values,
you can use this function.
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data(methylKit) # get percent methylation mat=percMethylation(methylBase.obj) # do some changes in the matrix # this is just a toy example # ideally you want to correct the matrix # for batch effects mat[mat==100]=80 # reconstruct the methylBase from the corrected matrix newobj=reconstruct(mat,methylBase.obj)
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