plotHR: Forest plot of hazard ratios

In TNBC.CMS: TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes

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)

TNBC.CMS documentation built on Nov. 8, 2020, 7:53 p.m.