SelectReferenceSetFromReadCounts {CNVPanelizer}R Documentation

SelectReferenceSetFromReadCounts

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")
[Package CNVPanelizer version 1.14.0 Index]