ReportTables: ReportTables

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

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.

Author(s)

Thomas Wolf, Cristiano Oliveira

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)

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