Amplicon-wise call of copy number alterations

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Description

Call of significant copy number alterations including different methods to correct for multiple hypothesis testing

Usage

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call.amplicons(CN, direction = "gain", method.p = "p_samples", thres.p = 0.05)

Arguments

CN

Matrix of copy numbers with attributes as decribed in calculate.CN.

direction

Detection of gene amplifications ("gain") or gene deletions ("loss").

method.p

Usage of uncorrected p-values ("p"), p-values corrected for samples ("p_samples") or p-values corrected for samples and amplicons ("p_samples_amplicons").

thres.p

Significance level for calling of copy number alterations.

Value

Indicator matrix with the detected copy number alterations in each amplicon ("amplicon") and in each sample ("sample") as attributes.

Examples

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## Not run: 
data(coverage)
CN <- calculate.CN(coverage)
calls <- call.amplicons(CN, direction="gain")

## End(Not run)