SelectReferenceSetFromReadCounts {CNVPanelizer} | R Documentation |
Select a reference set from read counts
SelectReferenceSetFromReadCounts(allSamplesReadCounts, normalizationMethod = "tmm", referenceMaximumNumberOfElements = 30, referenceSelectionMethod = "kmeans", lowerBoundPercentage = 1, upperBoundPercentage = 99)
allSamplesReadCounts |
All samples read counts matrix |
normalizationMethod |
tmm (trimmed mean of m values) or tss (total sum scaling) |
referenceMaximumNumberOfElements |
Maximum number of elements to consider as reference (only to be used in case interquantile reference selection method) |
referenceSelectionMethod |
Reference selection method ("kmeans", ...) |
lowerBoundPercentage |
Lower bound percentage (only to be used in case interquantile reference selection method) |
upperBoundPercentage |
Upper bound percentage (only to be used in case interquantile reference selection method) |
Returns a list of sample identifiers to be used as reference
Cristiano Oliveira
SelectReferenceSetFromReadCounts(allSamplesReadCounts, normalizationMethod = "tmm", referenceMaximumNumberOfElements = 30, referenceSelectionMethod = "kmeans")