plotGeneHist {oncomix} | R Documentation

## Plot a histogram of gene expression values from tumor and adjacent normal tissue.

### Description

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.

### Usage

    plotGeneHist(mmParams, exprNml, exprTum, isof)

### Arguments

`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

### Value

Returns a histogram of the gene expression values from the two groups.

### 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)
    isof <- rownames(mmParams)[1]
    plotGeneHist(mmParams, exprNml, exprTum, isof)

[Package oncomix version 1.10.0 Index]