normalize-methods: Normalize nucleotide counts.

In gerstung-lab/deepSNV: Detection of subclonal SNVs in deep sequencing data.

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.

Usage

normalize(test, control, ...)

## S4 method for signature 'matrix,matrix'
normalize(test, control, round=TRUE, ...)

## S4 method for signature 'deepSNV,missing'
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.
...	Parameters passed to loess.
round	Logical. Should normalized counts be rounded to integers? Default=TRUE

Value

A deepSNV-class object.

Note

This feature is somewhat experimental and the results should be treated with care. Sometimes it can be better to leave the data unnormalized and use a model with greater dispersion instead.

Author(s)

Moritz Gerstung

Examples

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

gerstung-lab/deepSNV documentation built on June 3, 2022, 3:05 p.m.