CNVPanelizer (version 1.2.2)

ReportTables: ReportTables

Description

This function generates the final report of the CNV detection procedure. One data frame is generated for each sample of interest.

Usage

ReportTables(geneNames, samplesNormalizedReadCounts, referenceNormalizedReadCounts, bootList, backgroundNoise)

Arguments

geneNames

Describe geneNames here

samplesNormalizedReadCounts

Describe samplesNormalizedReadCounts here

referenceNormalizedReadCounts

Describe referenceNormalizedReadCounts here

bootList

A list as returned by the BootList function

backgroundNoise

A list of background noise as returned by the Background function

Value

Returns a list of tables, one for each sample of interest. Each of these tables contains numerical information of the aberration status of each gene. For a detailed description see the Vignette.

Examples

data(sampleReadCounts)
data(referenceReadCounts)
## Gene names should be same size as row columns
geneNames <- row.names(referenceReadCounts)

ampliconNames <- NULL

normalizedReadCounts <- CombinedNormalizedCounts(sampleReadCounts,
                                                 referenceReadCounts,
                                                 ampliconNames = ampliconNames)

# After normalization data sets need to be splitted again to perform bootstrap
samplesNormalizedReadCounts = normalizedReadCounts["samples"][[1]]
referenceNormalizedReadCounts = normalizedReadCounts["reference"][[1]]

# Should be used values above 10000
replicates <- 10

# Perform the bootstrap based analysis
bootList <- BootList(geneNames,
                     samplesNormalizedReadCounts,
                     referenceNormalizedReadCounts,
                     replicates = replicates)

backgroundNoise = Background(geneNames,
                             samplesNormalizedReadCounts,
                             referenceNormalizedReadCounts,
                             bootList,
                             replicates = replicates)

reportTables <- ReportTables(geneNames,
             samplesNormalizedReadCounts,
             referenceNormalizedReadCounts,
             bootList,
             backgroundNoise)