CombinedNormalizedCounts: CombinedNormalizedCounts
In CNVPanelizer: Reliable CNV detection in targeted sequencing applications

Description Usage Arguments Value Author(s) Examples

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

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

`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

A list object with two matrices

`samples`	The samples matrix normalized
`reference`	The reference matrix normalized

Cristiano Oliveira, Thomas Wolf

data(sampleReadCounts)
data(referenceReadCounts)

normalizedReadCounts <- CombinedNormalizedCounts(sampleReadCounts,
                                                 referenceReadCounts)