CombinedNormalizedCounts: CombinedNormalizedCounts

In biostuff/CNVPanelizer: Reliable CNV detection in targeted sequencing applications

Description

This function makes use of Total sum scaling or NOISeq::tmm to normalize the read counts of all samples and references to the same median read count

Usage

    CombinedNormalizedCounts(sampleCounts,
                            referenceCounts,
                            method,
                            ampliconNames = NULL)

Arguments

sampleCounts	Matrix or vector with sample read counts (rows: amplicons, columns: samples)
referenceCounts	Matrix with reference read counts (rows: amplicons, columns: samples)
method	either "tmm" (trimmed mean of m values) or "tss"(total sum scaling)
ampliconNames	A vector with amplicon defining names for the reference and sample matrices

Value

A list object with two matrices

samples	The samples matrix normalized
reference	The reference matrix normalized

Author(s)

Cristiano Oliveira, Thomas Wolf

Examples

data(sampleReadCounts)
data(referenceReadCounts)

normalizedReadCounts <- CombinedNormalizedCounts(sampleReadCounts,
                                                 referenceReadCounts)

biostuff/CNVPanelizer documentation built on May 12, 2019, 9:25 p.m.