CombinedNormalizedCounts {CNVPanelizer} | R Documentation |
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)