plotHR {TNBC.CMS} | R Documentation

## Forest plot of hazard ratios

### Description

Produces a forest plot of hazard ratios for each gene. Also draws a forest plot of subtype-specific hazard ratios.

### Usage

    plotHR(expr, gene.symbol, pred, time, event, by.subtype = TRUE)

### Arguments

`expr` | A `SummarizedExperiment` object or a matrix containig gene expression profiles. If input is a `SummarizedExperiment`, the first element in the assays list should be a matrix of gene expression. Rows and columns of the gene expression matrix correspond to genes and samples, respectively (rownames must be to gene symbols).
`gene.symbol` | A vector of gene symbols for which hazard ratios are computed.
`pred` | A vector of predicted consensus molecular subtypes.
`time` | A vector of the follow-up time.
`event` | A vector representing survival status (0 = alive, 1 = dead).
`by.subtype` | A logical to determine if subtype-specific hazard ratios are computed (default is TRUE).

### Value

A forest plot of hazard ratios.

### Examples

    # Load gene expression profiles and clinical information of TNBC samples
    data(GSE25055)
    DFS.status <- colData(GSE25055)$DFS.status
    DFS.month <- colData(GSE25055)$DFS.month

    # Predict consensus molecular subtypes of TNBC samples
    prediction <- predictCMS(expr = GSE25055)

    # Forest plot of hazard ratios for input genes
    plotHR(expr = GSE25055, gene.symbol = c("RECK", "RELN", "EHD4", "PRRX2"),
           pred = prediction, time = DFS.month, event = DFS.status,
           by.subtype = FALSE)

    # Subtype-specific forest plot of hazard ratios for input genes
    plotHR(expr = GSE25055, gene.symbol = c("RECK", "RELN", "EHD4", "PRRX2"),
           pred = prediction, time = DFS.month, event = DFS.status,
           by.subtype = TRUE)

[Package TNBC.CMS version 1.0.0 Index]