plotGeneHist: Plot a histogram of gene expression values from tumor and...

Description Usage Arguments Value See Also Examples

View source: R/oncoMix_two_component_mixture_models.R

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

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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

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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)

oncomix documentation built on Nov. 8, 2020, 5:39 p.m.