binning {methimpute} | R Documentation |
This page provides an overview of all methimpute binning functions.
binCounts(data, binsize) binPositions(data, binsize) binMethylome(data, binsize, contexts = "total", columns.average = NULL)
data |
A |
binsize |
The window size used for binning. |
contexts |
A character vector with contexts for which the binning will be done. |
columns.average |
A character vector with names of columns in |
A GRanges-class
object for binCounts
and binPostions
. A list()
of GRanges-class
objects for binMethylome
.
binCounts
: Get the aggregated number of counts in each bin (no context).
binPositions
: Get the number of cytosines in each bin (total and per context).
binMethylome
: Get number of cytosines and aggregated counts for the specified contexts.
## Get some toy data file <- system.file("data","arabidopsis_toydata.RData", package="methimpute") data <- get(load(file)) print(data) ## Bin the data in various ways binCounts(data, binsize=1000) binPositions(data, binsize=1000) binMethylome(data, binsize=1000, contexts=c("total", "CG"), columns.average=NULL)