normalizeCounts: Normalize counts

View source: R/normalizeCounts.R

normalizeCountsR Documentation

Normalize counts

Description

This function performs a non-linear normalization of counts with respect to a reference sample (geometric mean)

Usage

normalizeCounts(object, control, span = 1, ...)

Arguments

object

an epigraHMMDataSet

control

list of control arguments from controlEM()

span

the span parameter of loessFit (default is 1)

...

arguments to be passed to loessFit for loess calculation

Details

This function 'limma::loessFit', which simply a wrapper for the 'stats::lowess' smoother.

Value

An epigraHMMDataSet with an 'offsets' assay filled in.

Author(s)

Pedro L. Baldoni, pedrobaldoni@gmail.com

References

https://github.com/plbaldoni/epigraHMM

Examples


# 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)


plbaldoni/epigraHMM documentation built on Oct. 15, 2023, 7:53 p.m.