deepSNV (version 1.18.3)

normalize: Normalize nucleotide counts.

Description

This functions performs a loess normalization of the nucleotide. This experimental feature can be used to compare experiments from different libraries or sequencing runs that may have differing noise characteristics.

Normalize nucleotide counts.

Normalize nucleotide counts.

Usage

normalize(test, control, ...)
"normalize"(test, control, round=TRUE, ...)
"normalize"(test, control,  ...)

Arguments

test

Either an deepSNV-class object or a named matrix with nucleotide counts.

control

Missing if test is an link{deepSNV-class} object, otherwise a matrix with nucleotide counts.

round

Logical. Should normalized counts be rounded to integers? Default=TRUE

...

Parameters passed to loess.

Value

A deepSNV-class object.

Examples

data(phiX, package = "deepSNV")
plot(phiX)
phiN <- normalize(phiX, round = TRUE)
plot(phiN)