CNVPanelizerFromReadCountsHelper: CNVPanelizerFromReadCountsHELPER

Description Usage Arguments Value Author(s) Examples

Description

Helper to performs the workflow analysis with CNVPanelizer from the read counts and splitting the batch of samples analyzed

Usage

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            CNVPanelizerFromReadCountsHELPER(sampleReadCounts,
                                             referenceReadCounts,
                                             genomicRangesFromBed,
                                             numberOfBootstrapReplicates = 10000,
                                             normalizationMethod = "tmm",
                                             robust = TRUE,
                                             backgroundSignificanceLevel = 0.05,
                                             outputDir = file.path(getwd(), "CNVPanelizer"),
                                             splitSize = 5)

Arguments

sampleReadCounts

samples read counts matrix

referenceReadCounts

reference read counts matrix

genomicRangesFromBed

genomic ranges from bed

numberOfBootstrapReplicates

number of bootstrap replicates

normalizationMethod

Normalization method ("tmm" or "tss")

robust

if TRUE, the median is used instead of mean

backgroundSignificanceLevel

The background Significance Level

outputDir

Output directory

splitSize

Split size of the batches analyzed

Value

Returns a list with the results of each samples analyzed

Author(s)

Cristiano Oliveira

Examples

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            CNVPanelizerFromReadCountsHELPER(sampleReadCounts,
                                             referenceReadCounts,
                                             genomicRangesFromBed,
                                             numberOfBootstrapReplicates = 10000,
                                             normalizationMethod = "tmm",
                                             robust = TRUE,
                                             backgroundSignificanceLevel = 0.05,
                                             outputDir = file.path(getwd(), "CNVPanelizer"),
                                             splitSize = 5)
    

budczies/CNVPanelizer documentation built on Nov. 20, 2018, 12:24 a.m.