smoothCoxph_man: Create a correlation of gene expression to log hazard ratio

In w2felix/TCGADataFelix: Analyzing the TCGA Data according to gene expression and survival

Description

Create a correlation of gene expression to log hazard ratio

Usage

smoothCoxph_man(x, Eset, exclude_values, xlimit, ylimit, xlabel, ylabel,
  logrisk = TRUE, survival = "overall", average = "median", ...)

Arguments

x	1 or multiple Genes, as a character vector list, to analyze
Eset	The Expression Set, containing the expression data in columns and the survival indicators in the columns X_OS and X_OS_IND
exclude_values	add a vector with following style c("column of clinical data to look for exclusion", "exclude group 1 from this column", "exclude group 2 from this column", ...)
xlimit	Manually define the x-axis limit
ylimit	Manually define the y-axis limit
xlabel	Manually define the x-axis label
ylabel	manually define the y-axis label
logrisk	don't exactly know... need to check
survival	"overall", "DFS"
average	values: 'mean' or 'median', defines how >1 genes are averaged
...	additional variables that can be added

Value

Plots the log Hazard ratio in correlation to its relative gene expression level using ggplot2

Examples

## Not run: 
smoothCoxph_man(x = c("BAMBI", "CD44"), Eset=Eset,
exclude_values=c("pathologic_stage", "Stage II", "Stage I", "Stage IV"),
logrisk=T, average="median")

## End(Not run)

w2felix/TCGADataFelix documentation built on May 19, 2019, 8:24 a.m.