topGeneQuants {oncomix} | R Documentation |
This function allows you to subset genes that are above pre-specified quantiles and that most closely resemble the distribution of oncogenes.
topGeneQuants(mmParams, deltMu2Thr = 90, deltMu1Thr = 10, siThr = 0.99)
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. |
Returns a dataframe containing all genes meeting the prespecified thresholds.
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)