SelectReferenceSetFromReadCounts: SelectReferenceSetFromReadCounts

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

Description

Select a reference set from read counts

Usage

SelectReferenceSetFromReadCounts(allSamplesReadCounts,
                                 normalizationMethod = "tmm",
                                 referenceMaximumNumberOfElements = 30,
                                 referenceSelectionMethod = "kmeans",
                                 lowerBoundPercentage = 1,
                                 upperBoundPercentage = 99)

Arguments

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)

Value

Returns a list of sample identifiers to be used as reference

Author(s)

Cristiano Oliveira

Examples

    
    
SelectReferenceSetFromReadCounts(allSamplesReadCounts,
                                 normalizationMethod = "tmm",
                                 referenceMaximumNumberOfElements = 30,
                                 referenceSelectionMethod = "kmeans")
    

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