topGeneQuants: Identify genes that meet pre-specified quantiles

Description Usage Arguments Value See Also Examples

Description

This function allows you to subset genes that are above pre-specified quantiles and that most closely resemble the distribution of oncogenes.

Usage

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topGeneQuants(mmParams, deltMu2Thr = 90, deltMu1Thr = 10, siThr = 0.99)

Arguments

mmParams

The output from the mixModelParams function.

deltMu2Thr

The percentile threshold for the deltaMu2 statistic. All genes exceeding this percentile threshold will be selected.

deltMu1Thr

The percentile threshold for the deltaMu1 statistic. All genes exceeding this percentile threshold will be selected.

siThr

The threshold for the selectivity index statistic (between 0-1). All genes exceeding this threshold will be selected.

Value

Returns a dataframe containing all genes meeting the prespecified thresholds.

See Also

mixModelParams

Examples

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exprNml <- as.data.frame(matrix(data=rgamma(n=150, shape=2, rate=2),
nrow=10, ncol=15))
colnames(exprNml) <- paste0("patientN", seq_len(ncol(exprNml)))
rownames(exprNml) <- paste0("gene", seq_len(nrow(exprNml)))

exprTum <- as.data.frame(matrix(data=rgamma(n=150, shape=4, rate=3),
nrow=10, ncol=15))
colnames(exprTum) <- paste0("patientT", seq_len(ncol(exprTum)))
rownames(exprTum) <- paste0("gene", seq_len(nrow(exprTum)))

mmParams <- mixModelParams(exprNml, exprTum)
topGeneQuants(mmParams)

oncomix documentation built on Nov. 8, 2020, 5:39 p.m.