Description Usage Arguments Value Examples
Copy number alteration calling after (possible) multiple testing correction for samples and/or amplicons/genes. P-values are controlled either for the number of samples, the number of amplicons/genes or both. Different methods of multiple testing can be chosen to control either FWER or FDR.
1 2 | call.CNA(CNA, analysis.mode="gene-wise", method.p="samples_genes/amplicons",
method.mt="bonferroni", thres.p=0.05, sig.call=0, sig.per=0)
|
CNA |
List of CNA assessments generated by |
analysis.mode |
The Mode of the analysis: ( |
method.p |
The multiple testing method used for detection:
Usage of uncorrected p-values ( |
method.mt |
Method for multiple testing correction: must be equal to |
thres.p |
Significance level for calling of copy number alterations. |
sig.call |
An integer >= 0. Only used if |
sig.per |
An integer >= 0. Only used if |
Table containing the status (GAIN, LOSS or NORMAL) of each amplicon or gene in each sample ("tab"
). Matrix of copy number estimates in each sample and each amplicon or gene ("CN"
). Indicator matrix of detected gains in each sample and each amplicon or gene ("gain"
) and the same for losses ("loss"
).
1 2 3 4 5 6 7 | ## Not run:
data(coverage)
CN <- calculate.CN(coverage)
CNA <- assess(CN)
calls <- call.CNA(CNA)
## End(Not run)
|
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