plotGeneHist {oncomix} | R Documentation |
This function allows you to plot a histogram of gene expression values from tumor and adjacent normal tissue with the option of including the best fitting Gaussian curve.
plotGeneHist(mmParams, exprNml, exprTum, isof)
mmParams |
The output from the getMixModelParams function. |
exprNml |
A dataframe (S3 or S4), matrix, or SummarizedExperiment object containing normal data with patients as columns and genes as rows. |
exprTum |
A dataframe (S3 or S4), matrix, or SummarizedExperiment object containing tumor data with patients as columns and genes as rows. |
isof |
The gene isoform to visualize |
Returns a histogram of the gene expression values from the two groups.
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) isof <- rownames(mmParams)[1] plotGeneHist(mmParams, exprNml, exprTum, isof)