topGeneQuants {oncomix} | R Documentation

## Identify genes that meet pre-specified quantiles

### Description

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

### Usage

    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

    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)

[Package oncomix version 1.9.0 Index]