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

Description Usage Arguments Value Author(s) Examples

View source: R/FolderAnalysis_functions.R

Select a reference set using Kmeans

1
2
3

    SelectReferenceSetByKmeans(allSamplesReadCounts,
			       normalizationMethod = "tmm",
			       referenceNumberOfElements)

`allSamplesReadCounts`	All samples read counts matrix
`normalizationMethod`	tmm (trimmed mean of m values) or tss (total sum scaling)
`referenceNumberOfElements`	Number of elements to select for the reference set

Returns a list of sample identifiers to be used as reference

Cristiano Oliveira

    
    
    SelectReferenceSetByKmeans(allSamplesReadCounts, 
                               normalizationMethod = "tmm", 
                               referenceNumberOfElements)