normalizeCounts {epigraHMM} | R Documentation |
This function performs a non-linear normalization of counts with respect to a reference sample (geometric mean)
normalizeCounts(object, control, span = 1, ...)
object |
an epigraHMMDataSet |
control |
list of control arguments from controlEM() |
span |
the span parameter of |
... |
arguments to be passed to |
This function 'limma::loessFit', which simply a wrapper for the 'stats::lowess' smoother.
An epigraHMMDataSet with an 'offsets' assay filled in.
Pedro L. Baldoni, pedrobaldoni@gmail.com
https://github.com/plbaldoni/epigraHMM
# Creating dummy object countData <- list('counts' = matrix(rpois(1e5,10),ncol = 2), 'controls' = matrix(rpois(1e5,5),ncol = 2)) colData <- data.frame(condition = c('A','A'), replicate = c(1,2)) object <- epigraHMMDataSetFromMatrix(countData,colData) # Normalizing counts object <- normalizeCounts(object = object,control = controlEM(), span = 1)