normalize-methods: Normalize nucleotide counts.

In mg14/deepSNV-old: Detection of subclonal SNVs in deep sequencing data.

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, ...)

## 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.
round	Logical. Should normalized counts be rounded to integers? Default=TRUE
...	Parameters passed to loess.

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)

mg14/deepSNV-old documentation built on May 22, 2019, 8:52 p.m.