ReportTables: ReportTables

Description Usage Arguments Value Author(s) Examples

View source: R/FolderAnalysis_functions.R

Description

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

Usage

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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.

Author(s)

Thomas Wolf, Cristiano Oliveira

Examples

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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)

CNVPanelizer documentation built on Nov. 8, 2020, 6:47 p.m.