ioncopy (version 2.2.2)

call.CNA: Gene-wise or amplicon-wise calling of copy number alterations

Description

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.

Usage

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)

Arguments

CNA

List of CNA assessments generated by assess.CNA.

analysis.mode

The Mode of the analysis: ("gene-wise") or ("amplicon-wise")

method.p

The multiple testing method used for detection: Usage of uncorrected p-values ("p"), p-values corrected for samples ("p_samples"), p-values corrected for amplicons/genes ("p_genes/amplicons") or p-values corrected for samples and amplicons/genes ("p_samples_genes/amplicons").

method.mt

Method for multiple testing correction: must be equal to bonferroni, holm, hochberg, fdr, BH, BY, hommel or none as described in the package stats.

thres.p

Significance level for calling of copy number alterations.

sig.call

An integer >= 0. Only used if analysis.mode="gene-wise". Required minimum number of amplicons supporting a gene CNA call.

sig.per

An integer >= 0. Only used if analysis.mode="gene-wise". Required minimum percentage of amplicons supporting a gene CNA call.

Value

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").

Examples

# NOT RUN {
data(coverage)
CN <- calculate.CN(coverage)
CNA <- assess(CN)
calls <- call.CNA(CNA)
# }