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 1.14.0 Index]